Here we’ll use the Bray-Curtis index to identify sample replicates (within each locus) that are more dissimilar than similar to the other replicates. Dissimilarity can be an indication of an issue (contamination, etc.) with a particular replicate.

This uses the output from the species-occupancy detection modeling in 03-species-occupancy-model.Rmd The occupancy modeling uses the ASVs (not taxonomy) and I’ll use a similar approach here with the Bray-Curtis and NMDS analyses.

Process

The process is a bit cumbersome because it requires looking at each sample/locus/replicate for the full reference DNA pool and vouchered reference pool.

The process for looking at the dissimilarity among replicates is to: 1. Read in data that has been cleaned up using the occupancy modeling 2. Create a community matrix (per locus) 3. Standardize data across replicates (fct decostand) 4. Generate Bray-Curtis distances (fct vegdist) 4a. Are any replicates more dissimilar than similar? 5. Generate NMDS plots from distance matrix (fct metaMDS)

Outputs

Based on the NMDS plots and Bray-Curtis dissimilarity index, I generated a list of samples to remove:

../data/reference_pool_dissimilarity_samples_to_remove.csv

The data that were used to generate that list are output .csv files from the Bray-Curtis function, implemented below.

In addition, three loci had insufficient data across all 18 samples in both the vouchered and full reference pools to be included in these analyses and will be dropped from further analyses:

16Sfish teleo crust2

source("../R/metabarcoding-funcs.R")
library(tidyverse)
library(stringi)
library(vegan)
library(reshape2)
library(textshape)
library(rlist)


# output from the ASV filtering based on the SODM for 
# vouchered ref
vrp_sodm_filtered_df <- readRDS("../data/voucher_features_sodm_filtered_taxonomy_df.rds")

# full reference
frp_sodm_filtered_df <- readRDS("../data/full_reference_sodm_filtered_taxonomy_df.rds")

I have wrapped the Bray-Curis and NMDS up into a function called bray_nmds_complete which outputs a .csv file with the replicates that are > 0.49 dissimilar and generates an NMDS plot.

I’ll use that function with an lappy and the list of loci, since each locus will be analyzed separately.

To cycle over a list of the loci…

# grab the names of the loci from the full dataframe
locs <- frp_sodm_filtered_df %>%
  select(locus) %>%
  unique() %>%
  as.list()

# turn that into a list that could be cycled over
loc_list <- locs$locus

# make a separate list for the VRP samples
locs19 <- frp_sodm_filtered_df %>%
  select(locus) %>%
  unique() %>%
  filter(!locus %in% c("crust2", "16Sfish", "teleo")) %>%
  as.list()

# turn that into a list that could be cycled over
loc_list19 <- locs19$locus

Full Reference dataframe

# cycle over the list of loci for the full reference pool sample replicates
# using the bray-curtis function to test for dissimilarity
lapply(loc_list19, bray_nmds_complete, sodm_filtered_df = frp_sodm_filtered_df, sample = "FRP")
Run 0 stress 0.05032398 
Run 1 stress 0.05032594 
... Procrustes: rmse 0.001963745  max resid 0.004266198 
... Similar to previous best
Run 2 stress 0.06433189 
Run 3 stress 0.3209238 
Run 4 stress 0.227495 
Run 5 stress 0.05032713 
... Procrustes: rmse 0.00111975  max resid 0.002597424 
... Similar to previous best
Run 6 stress 0.05032779 
... Procrustes: rmse 0.002633749  max resid 0.005649633 
... Similar to previous best
Run 7 stress 0.06720142 
Run 8 stress 0.3209238 
Run 9 stress 0.06433195 
Run 10 stress 0.06989063 
Run 11 stress 0.102771 
Run 12 stress 0.06433192 
Run 13 stress 0.06720143 
Run 14 stress 0.06989068 
Run 15 stress 0.08181662 
Run 16 stress 0.05033157 
... Procrustes: rmse 0.003521328  max resid 0.007473747 
... Similar to previous best
Run 17 stress 0.06433196 
Run 18 stress 0.05032506 
... Procrustes: rmse 0.0005089887  max resid 0.001183118 
... Similar to previous best
Run 19 stress 0.06433186 
Run 20 stress 0.05032567 
... Procrustes: rmse 0.001884185  max resid 0.004092335 
... Similar to previous best
*** Solution reached

Run 0 stress 0.05227481 
Run 1 stress 0.1777184 
Run 2 stress 0.07170935 
Run 3 stress 0.1740507 
Run 4 stress 0.07171101 
Run 5 stress 0.05227457 
... New best solution
... Procrustes: rmse 0.001858273  max resid 0.003812068 
... Similar to previous best
Run 6 stress 0.03669723 
... New best solution
... Procrustes: rmse 0.08285406  max resid 0.2056512 
Run 7 stress 0.07170998 
Run 8 stress 0.05227633 
Run 9 stress 0.1672324 
Run 10 stress 0.05227504 
Run 11 stress 0.07170832 
Run 12 stress 0.1955433 
Run 13 stress 0.1777184 
Run 14 stress 0.07171085 
Run 15 stress 0.0522757 
Run 16 stress 0.071711 
Run 17 stress 0.05227607 
Run 18 stress 0.07170828 
Run 19 stress 0.07171016 
Run 20 stress 0.1740537 
Run 21 stress 0.03669809 
... Procrustes: rmse 0.0004412054  max resid 0.0008091596 
... Similar to previous best
*** Solution reached

Run 0 stress 0.001280727 
Run 1 stress 0.0008851493 
... New best solution
... Procrustes: rmse 0.02747565  max resid 0.05308799 
Run 2 stress 9.499491e-05 
... New best solution
... Procrustes: rmse 0.09213706  max resid 0.183262 
Run 3 stress 9.897523e-05 
... Procrustes: rmse 0.0002913263  max resid 0.0005779135 
... Similar to previous best
Run 4 stress 0.0008187765 
Run 5 stress 9.682415e-05 
... Procrustes: rmse 0.05278958  max resid 0.1071393 
Run 6 stress 9.846953e-05 
... Procrustes: rmse 0.2255152  max resid 0.4222329 
Run 7 stress 9.937463e-05 
... Procrustes: rmse 0.2058249  max resid 0.3857322 
Run 8 stress 9.804859e-05 
... Procrustes: rmse 0.2103496  max resid 0.3940449 
Run 9 stress 0.0001140746 
... Procrustes: rmse 0.1326229  max resid 0.2521839 
Run 10 stress 0.0005208338 
... Procrustes: rmse 0.009388914  max resid 0.01818415 
Run 11 stress 9.95845e-05 
... Procrustes: rmse 0.1594821  max resid 0.3010649 
Run 12 stress 9.792724e-05 
... Procrustes: rmse 0.03589823  max resid 0.07242845 
Run 13 stress 9.706015e-05 
... Procrustes: rmse 0.1558765  max resid 0.2945659 
Run 14 stress 0.000310356 
... Procrustes: rmse 0.1014804  max resid 0.1951773 
Run 15 stress 9.659121e-05 
... Procrustes: rmse 0.06800617  max resid 0.1320285 
Run 16 stress 9.92103e-05 
... Procrustes: rmse 0.008701921  max resid 0.01726798 
Run 17 stress 9.751976e-05 
... Procrustes: rmse 0.2089696  max resid 0.3915145 
Run 18 stress 0.001147709 
Run 19 stress 9.972157e-05 
... Procrustes: rmse 0.0579419  max resid 0.1178463 
Run 20 stress 9.17396e-05 
... New best solution
... Procrustes: rmse 0.002421848  max resid 0.004777992 
... Similar to previous best
*** Solution reached
stress is (nearly) zero: you may have insufficient data

some squared distances are negative and changed to zero

Run 0 stress 0.01793481 
Run 1 stress 0.02377418 
Run 2 stress 0.01793592 
... Procrustes: rmse 0.0002903769  max resid 0.0006526605 
... Similar to previous best
Run 3 stress 0.01793833 
... Procrustes: rmse 0.0008104507  max resid 0.001786647 
... Similar to previous best
Run 4 stress 0.02586193 
Run 5 stress 0.2690221 
Run 6 stress 0.01793677 
... Procrustes: rmse 0.0004574407  max resid 0.001019185 
... Similar to previous best
Run 7 stress 0.0306749 
Run 8 stress 0.02377422 
Run 9 stress 0.01793048 
... New best solution
... Procrustes: rmse 0.002429503  max resid 0.005138497 
... Similar to previous best
Run 10 stress 0.01793331 
... Procrustes: rmse 0.001956373  max resid 0.004138439 
... Similar to previous best
Run 11 stress 0.0179379 
... Procrustes: rmse 0.003182547  max resid 0.006853465 
... Similar to previous best
Run 12 stress 0.02585976 
Run 13 stress 0.01793783 
... Procrustes: rmse 0.003166088  max resid 0.006775573 
... Similar to previous best
Run 14 stress 0.02864909 
Run 15 stress 0.02377422 
Run 16 stress 0.02377464 
Run 17 stress 0.01793927 
... Procrustes: rmse 0.00339453  max resid 0.007268699 
... Similar to previous best
Run 18 stress 0.03067444 
Run 19 stress 0.2190095 
Run 20 stress 0.01793866 
... Procrustes: rmse 0.003295913  max resid 0.007055757 
... Similar to previous best
*** Solution reached

some squared distances are negative and changed to zero

Run 0 stress 0.1496671 
Run 1 stress 0.1634708 
Run 2 stress 0.1634708 
Run 3 stress 0.1468143 
... New best solution
... Procrustes: rmse 0.2448269  max resid 0.4339198 
Run 4 stress 0.1535343 
Run 5 stress 0.1535326 
Run 6 stress 0.1537343 
Run 7 stress 0.1596704 
Run 8 stress 0.1811272 
Run 9 stress 0.1536952 
Run 10 stress 0.1570088 
Run 11 stress 0.1496671 
Run 12 stress 0.1537174 
Run 13 stress 0.1535332 
Run 14 stress 0.1468143 
... New best solution
... Procrustes: rmse 7.581228e-07  max resid 1.057093e-06 
... Similar to previous best
Run 15 stress 0.1941469 
Run 16 stress 0.1894768 
Run 17 stress 0.163471 
Run 18 stress 0.1772823 
Run 19 stress 0.1634708 
Run 20 stress 0.1468143 
... Procrustes: rmse 1.652641e-06  max resid 2.629501e-06 
... Similar to previous best
*** Solution reached

Run 0 stress 0.07131921 
Run 1 stress 0.185523 
Run 2 stress 0.07071025 
... New best solution
... Procrustes: rmse 0.06502016  max resid 0.1428037 
Run 3 stress 0.1103686 
Run 4 stress 0.07132007 
Run 5 stress 0.07131933 
Run 6 stress 0.07131936 
Run 7 stress 0.07071025 
... New best solution
... Procrustes: rmse 3.940693e-06  max resid 6.483427e-06 
... Similar to previous best
Run 8 stress 0.3209238 
Run 9 stress 0.07071025 
... New best solution
... Procrustes: rmse 2.607509e-06  max resid 4.656192e-06 
... Similar to previous best
Run 10 stress 0.1103686 
Run 11 stress 0.1103687 
Run 12 stress 0.07131969 
Run 13 stress 0.1103686 
Run 14 stress 0.1223463 
Run 15 stress 0.07071025 
... Procrustes: rmse 2.058157e-05  max resid 3.238398e-05 
... Similar to previous best
Run 16 stress 0.07131985 
Run 17 stress 0.07131958 
Run 18 stress 0.1103687 
Run 19 stress 0.07071026 
... Procrustes: rmse 5.569717e-05  max resid 8.97981e-05 
... Similar to previous best
Run 20 stress 0.1223413 
*** Solution reached

Run 0 stress 0.03404271 
Run 1 stress 0.04241063 
Run 2 stress 0.04073004 
Run 3 stress 0.05391961 
Run 4 stress 0.05635849 
Run 5 stress 0.05464615 
Run 6 stress 0.03404193 
... New best solution
... Procrustes: rmse 0.0004868161  max resid 0.0006450974 
... Similar to previous best
Run 7 stress 0.04241149 
Run 8 stress 0.04127956 
Run 9 stress 0.05464688 
Run 10 stress 0.05464741 
Run 11 stress 0.04073003 
Run 12 stress 0.04073009 
Run 13 stress 0.05392019 
Run 14 stress 0.05391934 
Run 15 stress 0.05464615 
Run 16 stress 0.03404373 
... Procrustes: rmse 0.0007670957  max resid 0.001079974 
... Similar to previous best
Run 17 stress 0.04072995 
Run 18 stress 0.05464613 
Run 19 stress 0.05635845 
Run 20 stress 0.04073001 
*** Solution reached

Run 0 stress 0.001593672 
Run 1 stress 0.0004533559 
... New best solution
... Procrustes: rmse 0.007094137  max resid 0.0130032 
Run 2 stress 0.0008871839 
... Procrustes: rmse 0.002653471  max resid 0.003735267 
... Similar to previous best
Run 3 stress 9.946597e-05 
... New best solution
... Procrustes: rmse 0.002142816  max resid 0.002976221 
... Similar to previous best
Run 4 stress 9.305128e-05 
... New best solution
... Procrustes: rmse 0.0004708507  max resid 0.0007991972 
... Similar to previous best
Run 5 stress 9.299729e-05 
... New best solution
... Procrustes: rmse 0.0001144739  max resid 0.0002248952 
... Similar to previous best
Run 6 stress 0.1866276 
Run 7 stress 0.1866276 
Run 8 stress 9.636433e-05 
... Procrustes: rmse 1.473294e-05  max resid 2.72295e-05 
... Similar to previous best
Run 9 stress 0.1866276 
Run 10 stress 9.539976e-05 
... Procrustes: rmse 0.0001372894  max resid 0.0002256603 
... Similar to previous best
Run 11 stress 0.0001514991 
... Procrustes: rmse 0.0008454852  max resid 0.001399129 
... Similar to previous best
Run 12 stress 7.740948e-05 
... New best solution
... Procrustes: rmse 0.0001485035  max resid 0.0003484905 
... Similar to previous best
Run 13 stress 0.0002026789 
... Procrustes: rmse 0.001175126  max resid 0.001675374 
... Similar to previous best
Run 14 stress 0.0002389813 
... Procrustes: rmse 0.001398349  max resid 0.001986637 
... Similar to previous best
Run 15 stress 0.0007600335 
Run 16 stress 0.0009157349 
Run 17 stress 0.001005354 
Run 18 stress 0.0006401498 
Run 19 stress 0.1866276 
Run 20 stress 9.122697e-05 
... Procrustes: rmse 0.0001720985  max resid 0.0003684408 
... Similar to previous best
*** Solution reached
stress is (nearly) zero: you may have insufficient data

some squared distances are negative and changed to zero

Run 0 stress 0.004849781 
Run 1 stress 0.007793128 
Run 2 stress 0.007779583 
Run 3 stress 9.872685e-05 
... New best solution
... Procrustes: rmse 0.04608516  max resid 0.08171449 
Run 4 stress 0.2203411 
Run 5 stress 0.004849842 
Run 6 stress 0.007804921 
Run 7 stress 0.007776096 
Run 8 stress 0.007768048 
Run 9 stress 0.007874874 
Run 10 stress 0.004849765 
Run 11 stress 0.2628288 
Run 12 stress 9.856175e-05 
... New best solution
... Procrustes: rmse 0.0001823488  max resid 0.0002860683 
... Similar to previous best
Run 13 stress 0.3043874 
Run 14 stress 0.0004672985 
... Procrustes: rmse 0.001773592  max resid 0.003044729 
... Similar to previous best
Run 15 stress 0.007808896 
Run 16 stress 0.007787191 
Run 17 stress 0.007784496 
Run 18 stress 0.001954411 
Run 19 stress 0.007782754 
Run 20 stress 0.007784116 
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.002725987 
Run 1 stress 0.001598293 
... New best solution
... Procrustes: rmse 0.008666246  max resid 0.01570875 
Run 2 stress 0.002510566 
Run 3 stress 9.887145e-05 
... New best solution
... Procrustes: rmse 0.03239538  max resid 0.05894239 
Run 4 stress 9.009163e-05 
... New best solution
... Procrustes: rmse 0.0001627038  max resid 0.0002598752 
... Similar to previous best
Run 5 stress 8.039583e-05 
... New best solution
... Procrustes: rmse 9.294059e-05  max resid 0.0002149094 
... Similar to previous best
Run 6 stress 9.346512e-05 
... Procrustes: rmse 0.0001923068  max resid 0.0003924234 
... Similar to previous best
Run 7 stress 0.0007114696 
Run 8 stress 0.01220527 
Run 9 stress 8.288297e-05 
... Procrustes: rmse 0.0001455327  max resid 0.000279312 
... Similar to previous best
Run 10 stress 0.0002002628 
... Procrustes: rmse 0.004380793  max resid 0.008180704 
... Similar to previous best
Run 11 stress 0.003540765 
Run 12 stress 0.002632566 
Run 13 stress 0.001345479 
Run 14 stress 9.714506e-05 
... Procrustes: rmse 0.0009914852  max resid 0.002052403 
... Similar to previous best
Run 15 stress 0.007292963 
Run 16 stress 0.0007634434 
Run 17 stress 0.003274976 
Run 18 stress 0.001888589 
Run 19 stress 8.209626e-05 
... Procrustes: rmse 0.0002077218  max resid 0.0005049695 
... Similar to previous best
Run 20 stress 0.0007201802 
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.007061937 
Run 1 stress 0.006133232 
... New best solution
... Procrustes: rmse 0.04020321  max resid 0.06360244 
Run 2 stress 0.003945341 
... New best solution
... Procrustes: rmse 0.04675964  max resid 0.07348764 
Run 3 stress 0.003778913 
... New best solution
... Procrustes: rmse 0.02050278  max resid 0.03255848 
Run 4 stress 0.0004329439 
... New best solution
... Procrustes: rmse 0.05334419  max resid 0.08268353 
Run 5 stress 0.0004098361 
... New best solution
... Procrustes: rmse 0.001820381  max resid 0.00284126 
... Similar to previous best
Run 6 stress 0.006594832 
Run 7 stress 0.001424179 
Run 8 stress 0.0061523 
Run 9 stress 0.001503611 
Run 10 stress 0.00464189 
Run 11 stress 0.00196111 
Run 12 stress 0.00310235 
Run 13 stress 0.005356668 
Run 14 stress 0.0001327757 
... New best solution
... Procrustes: rmse 0.004379381  max resid 0.00677173 
... Similar to previous best
Run 15 stress 0.000516457 
... Procrustes: rmse 0.006050742  max resid 0.009392071 
Run 16 stress 0.003682546 
Run 17 stress 0.003664024 
Run 18 stress 0.006487141 
Run 19 stress 0.0006784865 
Run 20 stress 9.158779e-05 
... New best solution
... Procrustes: rmse 0.001409623  max resid 0.002104411 
... Similar to previous best
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.0006167596 
Run 1 stress 0.0007789301 
... Procrustes: rmse 0.09172011  max resid 0.1769081 
Run 2 stress 0.001121839 
Run 3 stress 0.0008820109 
... Procrustes: rmse 0.02945519  max resid 0.0741092 
Run 4 stress 0.001202145 
Run 5 stress 0.001281649 
Run 6 stress 0.0008621738 
... Procrustes: rmse 0.09580386  max resid 0.2495048 
Run 7 stress 0.001745402 
Run 8 stress 0.2517984 
Run 9 stress 0.001728913 
Run 10 stress 0.001715897 
Run 11 stress 0.0003773019 
... New best solution
... Procrustes: rmse 0.1020543  max resid 0.2116814 
Run 12 stress 0.190385 
Run 13 stress 0.002006578 
Run 14 stress 9.597716e-05 
... New best solution
... Procrustes: rmse 0.163036  max resid 0.3305894 
Run 15 stress 0.0006464816 
Run 16 stress 0.001721668 
Run 17 stress 9.735888e-05 
... Procrustes: rmse 0.1614917  max resid 0.3688607 
Run 18 stress 0.0001726412 
... Procrustes: rmse 0.03366803  max resid 0.07303108 
Run 19 stress 0.001927828 
Run 20 stress 0.0002863077 
... Procrustes: rmse 0.03872929  max resid 0.0835279 
Run 21 stress 9.993534e-05 
... Procrustes: rmse 0.1279387  max resid 0.3522714 
Run 22 stress 0.0006602949 
Run 23 stress 9.937423e-05 
... Procrustes: rmse 0.01826084  max resid 0.03797475 
Run 24 stress 9.306018e-05 
... New best solution
... Procrustes: rmse 0.1628553  max resid 0.3713916 
Run 25 stress 0.001290327 
Run 26 stress 0.000945505 
Run 27 stress 0.002120838 
Run 28 stress 9.245546e-05 
... New best solution
... Procrustes: rmse 0.1556283  max resid 0.3070008 
Run 29 stress 0.002042329 
Run 30 stress 9.283865e-05 
... Procrustes: rmse 0.1760775  max resid 0.3658075 
Run 31 stress 0.0006070544 
Run 32 stress 9.907401e-05 
... Procrustes: rmse 0.09214861  max resid 0.2023489 
Run 33 stress 9.099424e-05 
... New best solution
... Procrustes: rmse 0.01350967  max resid 0.03286582 
Run 34 stress 9.777701e-05 
... Procrustes: rmse 0.1216854  max resid 0.3112685 
Run 35 stress 0.0006025806 
Run 36 stress 0.001194515 
Run 37 stress 0.001263133 
Run 38 stress 9.9449e-05 
... Procrustes: rmse 0.1252961  max resid 0.2988486 
Run 39 stress 9.949342e-05 
... Procrustes: rmse 0.00778975  max resid 0.01943024 
Run 40 stress 0.0003813559 
... Procrustes: rmse 0.1336997  max resid 0.2686601 
Run 41 stress 0.0002976847 
... Procrustes: rmse 0.107867  max resid 0.2272832 
Run 42 stress 0.0004135365 
... Procrustes: rmse 0.1357839  max resid 0.3351115 
Run 43 stress 0.001705086 
Run 44 stress 0.190385 
Run 45 stress 9.94936e-05 
... Procrustes: rmse 0.1699359  max resid 0.338255 
Run 46 stress 0.001252003 
Run 47 stress 0.000952599 
Run 48 stress 8.803094e-05 
... New best solution
... Procrustes: rmse 0.02565628  max resid 0.0637466 
Run 49 stress 0.0007158958 
Run 50 stress 9.9366e-05 
... Procrustes: rmse 0.1410323  max resid 0.2704096 
*** No convergence -- monoMDS stopping criteria:
    32: no. of iterations >= maxit
    15: stress < smin
     1: stress ratio > sratmax
     2: scale factor of the gradient < sfgrmin
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.08220736 
Run 1 stress 0.1046338 
Run 2 stress 0.08220815 
... Procrustes: rmse 0.0005210259  max resid 0.000852318 
... Similar to previous best
Run 3 stress 0.09077278 
Run 4 stress 0.0822094 
... Procrustes: rmse 0.001866474  max resid 0.003013214 
... Similar to previous best
Run 5 stress 0.09077186 
Run 6 stress 0.07644664 
... New best solution
... Procrustes: rmse 0.2173407  max resid 0.4065968 
Run 7 stress 0.0922239 
Run 8 stress 0.07644676 
... Procrustes: rmse 0.000196478  max resid 0.0004129595 
... Similar to previous best
Run 9 stress 0.2382677 
Run 10 stress 0.09077153 
Run 11 stress 0.07644669 
... Procrustes: rmse 0.0001142272  max resid 0.0002356965 
... Similar to previous best
Run 12 stress 0.09803422 
Run 13 stress 0.09077179 
Run 14 stress 0.07644684 
... Procrustes: rmse 0.0002418747  max resid 0.0005041906 
... Similar to previous best
Run 15 stress 0.07644665 
... Procrustes: rmse 2.050792e-05  max resid 3.960642e-05 
... Similar to previous best
Run 16 stress 0.09077417 
Run 17 stress 0.2007841 
Run 18 stress 0.08221227 
Run 19 stress 0.07644664 
... Procrustes: rmse 3.7397e-06  max resid 7.186848e-06 
... Similar to previous best
Run 20 stress 0.09785412 
*** Solution reached

Run 0 stress 0.02704468 
Run 1 stress 0.02704507 
... Procrustes: rmse 0.0005381191  max resid 0.0007774085 
... Similar to previous best
Run 2 stress 0.1111581 
Run 3 stress 0.02704669 
... Procrustes: rmse 0.001076435  max resid 0.001620683 
... Similar to previous best
Run 4 stress 0.02704519 
... Procrustes: rmse 0.0005815017  max resid 0.0008398243 
... Similar to previous best
Run 5 stress 0.02704708 
... Procrustes: rmse 0.001172974  max resid 0.001769932 
... Similar to previous best
Run 6 stress 0.02704588 
... Procrustes: rmse 0.0008172933  max resid 0.001239776 
... Similar to previous best
Run 7 stress 0.1111585 
Run 8 stress 0.02704598 
... Procrustes: rmse 0.0008693736  max resid 0.001298837 
... Similar to previous best
Run 9 stress 0.1097378 
Run 10 stress 0.02704604 
... Procrustes: rmse 0.0008909887  max resid 0.001330815 
... Similar to previous best
Run 11 stress 0.02704449 
... New best solution
... Procrustes: rmse 0.0002472625  max resid 0.0004381706 
... Similar to previous best
Run 12 stress 0.02704766 
... Procrustes: rmse 0.001093556  max resid 0.00171918 
... Similar to previous best
Run 13 stress 0.02704643 
... Procrustes: rmse 0.0008397852  max resid 0.001284364 
... Similar to previous best
Run 14 stress 0.02704631 
... Procrustes: rmse 0.0008500115  max resid 0.001320229 
... Similar to previous best
Run 15 stress 0.1111587 
Run 16 stress 0.02704679 
... Procrustes: rmse 0.0009792526  max resid 0.0015229 
... Similar to previous best
Run 17 stress 0.02704623 
... Procrustes: rmse 0.0007882945  max resid 0.001232702 
... Similar to previous best
Run 18 stress 0.02704598 
... Procrustes: rmse 0.00070492  max resid 0.001108969 
... Similar to previous best
Run 19 stress 0.02704445 
... New best solution
... Procrustes: rmse 5.188721e-05  max resid 7.908923e-05 
... Similar to previous best
Run 20 stress 0.02704602 
... Procrustes: rmse 0.0008116506  max resid 0.001244635 
... Similar to previous best
*** Solution reached

Run 0 stress 0.07320908 
Run 1 stress 0.07320908 
... Procrustes: rmse 2.004045e-06  max resid 4.218397e-06 
... Similar to previous best
Run 2 stress 0.07320908 
... Procrustes: rmse 1.734825e-06  max resid 3.710366e-06 
... Similar to previous best
Run 3 stress 0.1761948 
Run 4 stress 0.1711538 
Run 5 stress 0.07320908 
... Procrustes: rmse 2.441523e-06  max resid 5.217772e-06 
... Similar to previous best
Run 6 stress 0.1457451 
Run 7 stress 0.07320908 
... Procrustes: rmse 1.23315e-06  max resid 2.397839e-06 
... Similar to previous best
Run 8 stress 0.1783525 
Run 9 stress 0.07320908 
... Procrustes: rmse 9.256728e-07  max resid 1.292366e-06 
... Similar to previous best
Run 10 stress 0.07320908 
... Procrustes: rmse 4.301807e-06  max resid 9.728604e-06 
... Similar to previous best
Run 11 stress 0.1596171 
Run 12 stress 0.07320908 
... Procrustes: rmse 1.932452e-06  max resid 4.214723e-06 
... Similar to previous best
Run 13 stress 0.07320908 
... Procrustes: rmse 1.539691e-06  max resid 3.252986e-06 
... Similar to previous best
Run 14 stress 0.1761967 
Run 15 stress 0.07320908 
... Procrustes: rmse 1.327486e-06  max resid 3.304982e-06 
... Similar to previous best
Run 16 stress 0.07320908 
... Procrustes: rmse 9.971043e-07  max resid 1.797971e-06 
... Similar to previous best
Run 17 stress 0.07320908 
... Procrustes: rmse 6.469091e-06  max resid 1.234083e-05 
... Similar to previous best
Run 18 stress 0.07320908 
... Procrustes: rmse 1.150321e-06  max resid 2.414092e-06 
... Similar to previous best
Run 19 stress 0.07320908 
... Procrustes: rmse 1.063947e-06  max resid 1.704786e-06 
... Similar to previous best
Run 20 stress 0.1761947 
*** Solution reached

Run 0 stress 0.0003690946 
Run 1 stress 0.2968929 
Run 2 stress 9.913093e-05 
... New best solution
... Procrustes: rmse 0.07085411  max resid 0.1516461 
Run 3 stress 9.999722e-05 
... Procrustes: rmse 0.0002201373  max resid 0.0004327531 
... Similar to previous best
Run 4 stress 9.575975e-05 
... New best solution
... Procrustes: rmse 0.0001794116  max resid 0.0004220792 
... Similar to previous best
Run 5 stress 9.260103e-05 
... New best solution
... Procrustes: rmse 0.0002044742  max resid 0.0003531156 
... Similar to previous best
Run 6 stress 0.0001600694 
... Procrustes: rmse 0.01505675  max resid 0.03167053 
Run 7 stress 0.0001596279 
... Procrustes: rmse 0.00032951  max resid 0.0006006541 
... Similar to previous best
Run 8 stress 9.769899e-05 
... Procrustes: rmse 3.782302e-05  max resid 6.067523e-05 
... Similar to previous best
Run 9 stress 0.2796297 
Run 10 stress 9.143806e-05 
... New best solution
... Procrustes: rmse 6.578362e-05  max resid 0.0001321742 
... Similar to previous best
Run 11 stress 0.001538226 
Run 12 stress 9.724414e-05 
... Procrustes: rmse 0.1357138  max resid 0.2768219 
Run 13 stress 9.933341e-05 
... Procrustes: rmse 0.06645189  max resid 0.1329136 
Run 14 stress 9.924928e-05 
... Procrustes: rmse 0.0002999558  max resid 0.0007423378 
... Similar to previous best
Run 15 stress 9.589022e-05 
... Procrustes: rmse 0.05518586  max resid 0.1180289 
Run 16 stress 0.001564066 
Run 17 stress 0.001468815 
Run 18 stress 8.110974e-05 
... New best solution
... Procrustes: rmse 0.0002767109  max resid 0.000640692 
... Similar to previous best
Run 19 stress 9.550164e-05 
... Procrustes: rmse 0.0001615734  max resid 0.0003296234 
... Similar to previous best
Run 20 stress 9.425705e-05 
... Procrustes: rmse 0.0002885959  max resid 0.0006592086 
... Similar to previous best
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.04781366 
Run 1 stress 0.04663982 
... New best solution
... Procrustes: rmse 0.2034987  max resid 0.4329019 
Run 2 stress 0.04663972 
... New best solution
... Procrustes: rmse 0.0001467378  max resid 0.0003408214 
... Similar to previous best
Run 3 stress 0.05351554 
Run 4 stress 0.05351514 
Run 5 stress 0.04781326 
Run 6 stress 0.04781314 
Run 7 stress 0.04781331 
Run 8 stress 0.0535149 
Run 9 stress 0.04663969 
... New best solution
... Procrustes: rmse 7.367476e-05  max resid 0.0001578297 
... Similar to previous best
Run 10 stress 0.0466398 
... Procrustes: rmse 0.0001488907  max resid 0.0002506899 
... Similar to previous best
Run 11 stress 0.04781314 
Run 12 stress 0.05351482 
Run 13 stress 0.04663977 
... Procrustes: rmse 0.0001342677  max resid 0.000256718 
... Similar to previous best
Run 14 stress 0.05351515 
Run 15 stress 0.04663976 
... Procrustes: rmse 0.0001266586  max resid 0.000213622 
... Similar to previous best
Run 16 stress 0.05351574 
Run 17 stress 0.04781315 
Run 18 stress 0.04663972 
... Procrustes: rmse 8.51421e-05  max resid 0.0001712532 
... Similar to previous best
Run 19 stress 0.04781349 
Run 20 stress 0.04663991 
... Procrustes: rmse 0.0002006478  max resid 0.0004887694 
... Similar to previous best
*** Solution reached

Run 0 stress 0.03852861 
Run 1 stress 0.1654582 
Run 2 stress 0.03852939 
... Procrustes: rmse 0.0004331954  max resid 0.001020602 
... Similar to previous best
Run 3 stress 0.03852895 
... Procrustes: rmse 0.0002270687  max resid 0.0005334849 
... Similar to previous best
Run 4 stress 0.0385288 
... Procrustes: rmse 0.0006556131  max resid 0.001548393 
... Similar to previous best
Run 5 stress 0.03852894 
... Procrustes: rmse 0.0007260868  max resid 0.001713027 
... Similar to previous best
Run 6 stress 0.03852912 
... Procrustes: rmse 0.0003170953  max resid 0.000746315 
... Similar to previous best
Run 7 stress 0.03852889 
... Procrustes: rmse 0.0002084362  max resid 0.0004895812 
... Similar to previous best
Run 8 stress 0.03852895 
... Procrustes: rmse 0.0002429794  max resid 0.000571497 
... Similar to previous best
Run 9 stress 0.2316853 
Run 10 stress 0.03852916 
... Procrustes: rmse 0.0003395288  max resid 0.0007998688 
... Similar to previous best
Run 11 stress 0.0385288 
... Procrustes: rmse 0.0001544866  max resid 0.0003631234 
... Similar to previous best
Run 12 stress 0.1573475 
Run 13 stress 0.03852853 
... New best solution
... Procrustes: rmse 8.128728e-05  max resid 0.0001926985 
... Similar to previous best
Run 14 stress 0.0385286 
... Procrustes: rmse 8.637044e-05  max resid 0.0002037003 
... Similar to previous best
Run 15 stress 0.03852865 
... Procrustes: rmse 0.0001313458  max resid 0.0003102947 
... Similar to previous best
Run 16 stress 0.03852888 
... Procrustes: rmse 0.0002692969  max resid 0.0006361657 
... Similar to previous best
Run 17 stress 0.03852901 
... Procrustes: rmse 0.0003519962  max resid 0.000831036 
... Similar to previous best
Run 18 stress 0.301734 
Run 19 stress 0.03852936 
... Procrustes: rmse 0.0005046  max resid 0.001191245 
... Similar to previous best
Run 20 stress 0.03852861 
... Procrustes: rmse 4.364481e-05  max resid 9.68068e-05 
... Similar to previous best
*** Solution reached

Run 0 stress 0.004375477 
Run 1 stress 0.2392124 
Run 2 stress 0.004386192 
... Procrustes: rmse 0.001463297  max resid 0.002544894 
... Similar to previous best
Run 3 stress 0.2944258 
Run 4 stress 0.004437502 
... Procrustes: rmse 0.006321878  max resid 0.0082149 
Run 5 stress 0.004428057 
... Procrustes: rmse 0.005960111  max resid 0.008000272 
Run 6 stress 0.04726353 
Run 7 stress 0.004389588 
... Procrustes: rmse 0.003529055  max resid 0.004949438 
... Similar to previous best
Run 8 stress 0.05574174 
Run 9 stress 0.202569 
Run 10 stress 0.004390746 
... Procrustes: rmse 0.001845977  max resid 0.003198968 
... Similar to previous best
Run 11 stress 0.04258046 
Run 12 stress 0.004447288 
... Procrustes: rmse 0.006643638  max resid 0.008701654 
Run 13 stress 0.004374636 
... New best solution
... Procrustes: rmse 0.0003986833  max resid 0.0005540125 
... Similar to previous best
Run 14 stress 0.04726461 
Run 15 stress 0.00464466 
... Procrustes: rmse 0.009726585  max resid 0.01382343 
Run 16 stress 0.04257692 
Run 17 stress 0.004386292 
... Procrustes: rmse 0.001850264  max resid 0.0030073 
... Similar to previous best
Run 18 stress 0.04258072 
Run 19 stress 0.00438586 
... Procrustes: rmse 0.002681347  max resid 0.003977501 
... Similar to previous best
Run 20 stress 0.05574241 
*** Solution reached

[[1]]
[[1]][[1]]
$sites
                PCoA1         PCoA2
FRP_3_2 -0.0077556760 -0.0004483978
FRP_1_1 -0.0074078032  0.0106175215
FRP_1_2  0.0136031448 -0.0045690012
FRP_1_3 -0.0003200055 -0.0033346282
FRP_2_1 -0.0084371322 -0.0055360574
FRP_2_2 -0.0114169252 -0.0009201659
FRP_2_3  0.0015782355 -0.0005754210
FRP_3_1  0.0138635685  0.0065993296
FRP_3_3  0.0062925933 -0.0018331796

$centroids
          PCoA1         PCoA2
1  0.0004802225 -1.930358e-03
2 -0.0076432259 -2.570950e-03
3  0.0055992833  8.032607e-05

attr(,"class")
[1] "ordiplot"

[[1]][[2]]
[[1]][[2]]$x
 [1] 0.013431725 0.022975729 0.013386603 0.012024594 0.009644468 0.011296132 0.024177681
 [8] 0.017863794 0.026378430 0.016655836 0.017323198 0.012602273 0.017200114 0.021926298
[15] 0.020100664 0.016227316 0.024348019 0.025619571 0.016398915 0.013476611 0.014177795
[22] 0.010969808 0.012970100 0.012118562 0.017715952 0.013157313 0.011247205 0.017141118
[29] 0.025668067 0.017769823 0.016486741 0.027339705 0.019960160 0.017643101 0.012066248
[36] 0.014492783

[[1]][[2]]$y
 [1] 0.010427283 0.032887161 0.011820674 0.011360892 0.004583008 0.014402034 0.033000873
 [8] 0.023190655 0.038356293 0.020785527 0.021514005 0.012368640 0.018327827 0.035162820
[15] 0.030117317 0.022600190 0.033659999 0.036596057 0.020028630 0.011985196 0.010509155
[22] 0.011611776 0.014534156 0.010184293 0.026005759 0.012219686 0.009717914 0.020447567
[29] 0.037578657 0.023152242 0.018816894 0.037401429 0.026545530 0.018600035 0.012648339
[36] 0.017118223

[[1]][[2]]$yf
 [1] 0.012041850 0.033677713 0.012041850 0.012041850 0.004583008 0.012041850 0.033677713
 [8] 0.024116219 0.037878861 0.020140084 0.020140084 0.012041850 0.020140084 0.033677713
[15] 0.030117317 0.020140084 0.033677713 0.036596057 0.020140084 0.012041850 0.012041850
[22] 0.010664845 0.012041850 0.012041850 0.024116219 0.012041850 0.010664845 0.020140084
[29] 0.037578657 0.024116219 0.020140084 0.037878861 0.026545530 0.020140084 0.012041850
[36] 0.017118223


[[1]][[3]]


[[2]]
[[2]][[1]]
$sites
              PCoA1       PCoA2
FRP_1_2  0.06494987 -0.06626920
FRP_1_3 -0.17107055 -0.13782173
FRP_2_1  0.01742536 -0.06481453
FRP_2_2  0.04168515 -0.15435207
FRP_2_3  0.05092583  0.06977421
FRP_3_1  0.31688597  0.14104534
FRP_3_2  0.14193101 -0.01935849
FRP_3_3 -0.28249217  0.15091566
FRP_1_1 -0.18024048  0.08088081

$centroids
        PCoA1       PCoA2
1 -0.09805807 -0.03627434
2  0.03708432 -0.06862697
3  0.10747934  0.05871270

attr(,"class")
[1] "ordiplot"

[[2]][[2]]
[[2]][[2]]$x
 [1] 0.3770429 0.2461778 0.2934774 0.3566584 0.4025635 0.2909018 0.4530425 0.3557978 0.3540150
[10] 0.3437761 0.4104616 0.5734886 0.4657150 0.3736381 0.3588538 0.2848001 0.3572875 0.4293202
[19] 0.3009628 0.4119583 0.3378513 0.3017814 0.4573734 0.3366396 0.4783606 0.3883292 0.4013016
[28] 0.3570193 0.4361997 0.3638602 0.3948414 0.6182536 0.5559321 0.5127856 0.3987264 0.2624794

[[2]][[2]]$y
 [1] 0.334923890 0.005658642 0.140255494 0.340264245 0.531499714 0.178170573 0.536509313
 [8] 0.383522919 0.329268820 0.398875287 0.550190144 0.866367654 0.512160068 0.350756245
[15] 0.318521286 0.141810879 0.341973484 0.537157960 0.183806244 0.532034888 0.379916624
[22] 0.200197848 0.512105206 0.207560446 0.499398350 0.323561187 0.536326572 0.350085330
[29] 0.525503008 0.347697515 0.354759139 1.009084275 0.829126316 0.693654514 0.525116058
[36] 0.182186706

[[2]][[2]]$yf
 [1] 0.349947236 0.005658642 0.160605913 0.349947236 0.527288522 0.160605913 0.527288522
 [8] 0.349947236 0.349947236 0.349947236 0.527288522 0.866367654 0.527288522 0.349947236
[15] 0.349947236 0.160605913 0.349947236 0.527288522 0.183806244 0.527288522 0.349947236
[22] 0.200197848 0.527288522 0.207560446 0.527288522 0.349947236 0.527288522 0.349947236
[29] 0.527288522 0.349947236 0.354759139 1.009084275 0.829126316 0.693654514 0.525116058
[36] 0.160605913


[[2]][[3]]


[[3]]
[[3]][[1]]
$sites
                PCoA1        PCoA2
FRP_2_2 -0.0056747798  0.017442242
FRP_3_1 -0.0056845971  0.008868028
FRP_1_3  0.0000209112 -0.018369993
FRP_1_2  0.0177420762 -0.023964050
FRP_1_1 -0.0199796633 -0.033721821
FRP_2_1 -0.0132891435 -0.005679593
FRP_2_3 -0.0095849868 -0.002671528
FRP_3_2 -0.0589465487  0.037203580
FRP_3_3  0.0953967317  0.020893134

$centroids
          PCoA1         PCoA2
1 -0.0005652555 -0.0240508147
2 -0.0100271030  0.0004877264
3 -0.0045067655  0.0114597151

attr(,"class")
[1] "ordiplot"

[[3]][[2]]
[[3]][[2]]$x
 [1] 0.05091691 0.05590369 0.06797155 0.06567495 0.05526485 0.05059249 0.07503465 0.10823322
 [9] 0.05284606 0.06149564 0.06280045 0.05829094 0.04529058 0.07657186 0.10925392 0.04760468
[17] 0.04780922 0.05436990 0.04867337 0.08710807 0.10712747 0.05919926 0.07133588 0.06231871
[25] 0.10158450 0.09683261 0.05873039 0.05624024 0.08593452 0.12899995 0.03647458 0.08302039
[33] 0.11866578 0.07924674 0.11292312 0.15642901

[[3]][[2]]$y
 [1] 1.557600e-05 3.329966e-05 5.940920e-05 4.957679e-05 2.900777e-05 1.318555e-05
 [7] 9.844787e-02 9.852615e-02 2.162918e-05 4.643252e-05 4.157737e-05 2.827331e-05
[13] 1.707781e-05 9.846189e-02 9.853335e-02 2.617719e-05 2.127856e-05 2.171337e-05
[19] 2.484331e-05 9.848101e-02 9.852379e-02 2.279351e-05 4.276256e-05 5.059855e-05
[25] 9.850718e-02 9.852446e-02 2.464809e-05 3.759857e-05 9.849275e-02 9.850640e-02
[31] 1.582388e-05 9.846810e-02 9.850596e-02 9.845696e-02 9.851686e-02 1.372496e-01

[[3]][[2]]$yf
 [1] 2.021212e-05 2.932263e-05 5.108588e-05 4.957679e-05 2.900777e-05 2.021212e-05
 [7] 9.844787e-02 9.851875e-02 2.162918e-05 4.620281e-05 4.620281e-05 2.932263e-05
[13] 1.707781e-05 9.845942e-02 9.851875e-02 2.021212e-05 2.021212e-05 2.171337e-05
[19] 2.021212e-05 9.848688e-02 9.851875e-02 2.932263e-05 5.108588e-05 4.620281e-05
[25] 9.851582e-02 9.851582e-02 2.932263e-05 2.932263e-05 9.848688e-02 9.851875e-02
[31] 1.582388e-05 9.846810e-02 9.851875e-02 9.845942e-02 9.851875e-02 1.372496e-01


[[3]][[3]]


[[4]]
[[4]][[1]]
$sites
               PCoA1         PCoA2
FRP_2_2 -0.262240453 -0.0038533877
FRP_3_1  0.008729208  0.2002859672
FRP_2_1 -0.173286965  0.0947070670
FRP_2_3 -0.056933156  0.0339735572
FRP_1_2  0.411606057 -0.1217504500
FRP_3_2 -0.263052267 -0.1718486962
FRP_3_3  0.460902494  0.0289761450
FRP_1_1 -0.117304324 -0.0608939723
FRP_1_3 -0.008420595  0.0004037698

$centroids
         PCoA1        PCoA2
1 -0.003826581 -0.009450722
2 -0.151869651  0.051668726
3  0.028573925  0.131970064

attr(,"class")
[1] "ordiplot"

[[4]][[2]]
[[4]][[2]]$x
 [1] 0.3666786 0.2745743 0.2846767 0.6936960 0.2460870 0.7395843 0.3220790 0.3384186 0.2934343
[10] 0.2606911 0.5440963 0.4580087 0.4636392 0.3434786 0.2499468 0.1881074 0.6220386 0.3746198
[19] 0.6702217 0.1862354 0.2540122 0.5142405 0.3486079 0.5204338 0.1581332 0.1529300 0.7029519
[28] 0.1684395 0.5477143 0.4507136 0.7471961 0.2733190 0.3668404 0.6078074 0.4970476 0.1677923

[[4]][[2]]$y
 [1] 0.6316655 0.3277121 0.3825655 1.3261435 0.3210455 1.3827627 0.3179736 0.4917713 0.3343206
[10] 0.3714421 0.9791760 0.8521754 0.9008778 0.4885665 0.3163162 0.3051013 1.2069735 0.6118285
[19] 1.1910199 0.3564847 0.3602581 0.9547932 0.5036826 1.0004253 0.1209086 0.1116373 1.3048853
[28] 0.3219594 1.0098201 0.8599778 1.4340853 0.3852232 0.6060120 1.0859949 0.8912121 0.2211410

[[4]][[2]]$yf
 [1] 0.6165020 0.3542136 0.3542136 1.3155144 0.3247369 1.3827627 0.3542136 0.4901689 0.3542136
[10] 0.3542136 0.9898007 0.8560766 0.8960449 0.4901689 0.3247369 0.3247369 1.1989967 0.6165020
[19] 1.1989967 0.3247369 0.3542136 0.9547932 0.5036826 0.9898007 0.1209086 0.1116373 1.3155144
[28] 0.3219594 1.0098201 0.8560766 1.4340853 0.3542136 0.6165020 1.0859949 0.8960449 0.2211410


[[4]][[3]]


[[5]]
[[5]][[1]]
$sites
              PCoA1       PCoA2
FRP_1_1 -0.04014545  0.01465985
FRP_1_3  0.09254271 -0.03301385
FRP_2_1 -0.03086299 -0.02900160
FRP_2_2 -0.03078452 -0.11866051
FRP_2_3 -0.06272215 -0.01747867
FRP_3_1  0.02047142  0.11706061
FRP_3_2 -0.10791489  0.02973555
FRP_1_2  0.14426116 -0.01350986
FRP_3_3  0.01515471  0.05020848

$centroids
        PCoA1       PCoA2
1  0.08707240 -0.02117427
2 -0.05221464 -0.03602501
3 -0.01946476  0.06400382

attr(,"class")
[1] "ordiplot"

[[5]][[2]]
[[5]][[2]]$x
 [1] 0.1883248 0.2004467 0.1989875 0.1351847 0.2161442 0.1576516 0.2252707 0.0962406 0.1687482
[10] 0.1823747 0.1696022 0.1996427 0.2241094 0.1154127 0.1124088 0.1934365 0.1220679 0.2061328
[19] 0.1790426 0.2313514 0.1690148 0.1168174 0.2464477 0.1688671 0.2074800 0.2053333 0.1738575
[28] 0.0711903 0.2102079 0.0945083 0.1679886 0.1947591 0.1395905 0.2599633 0.1352807 0.1557269

[[5]][[2]]$y
 [1] 0.16365380 0.21766030 0.10640470 0.13874779 0.28312227 0.22490608 0.26583439 0.09902492
 [9] 0.19589003 0.23199901 0.18075942 0.17382419 0.27612345 0.10576822 0.08049805 0.18291730
[17] 0.08823767 0.12849952 0.11207748 0.27108802 0.15253616 0.09649341 0.28956095 0.13974590
[25] 0.33749225 0.15166241 0.19535845 0.09955983 0.27859812 0.10874032 0.24026448 0.19568789
[33] 0.18760538 0.36751655 0.20801396 0.18582984

[[5]][[2]]$yf
 [1] 0.1787648 0.1787648 0.1787648 0.1387478 0.2853764 0.1787648 0.2853764 0.0969032 0.1787648
[10] 0.1787648 0.1787648 0.1787648 0.2853764 0.0969032 0.0969032 0.1787648 0.0969032 0.1787648
[19] 0.1787648 0.2853764 0.1787648 0.0969032 0.2895609 0.1787648 0.2853764 0.1787648 0.1787648
[28] 0.0969032 0.2853764 0.0969032 0.1787648 0.1787648 0.1787648 0.3675166 0.1787648 0.1787648


[[5]][[3]]


[[6]]
[[6]][[1]]
$sites
               PCoA1        PCoA2
FRP_3_3 -0.008256521  0.002439797
FRP_2_2  0.042079766 -0.022582048
FRP_1_1 -0.098491142  0.005826303
FRP_2_1  0.022435380  0.042716838
FRP_1_3  0.003608971 -0.014881121
FRP_2_3  0.061202512  0.009883980
FRP_3_1  0.018025745 -0.041081332
FRP_1_2 -0.006717833  0.050579740
FRP_3_2 -0.033886879 -0.032902156

$centroids
         PCoA1       PCoA2
1 -0.023867074  0.01500425
2  0.045217987  0.00856103
3 -0.008985759 -0.02340007

attr(,"class")
[1] "ordiplot"

[[6]][[2]]
[[6]][[2]]$x
 [1] 0.08073536 0.10557947 0.06776137 0.08273844 0.09263127 0.08021865 0.09759218 0.07580858
 [9] 0.14715290 0.08704157 0.08109290 0.06877224 0.06375325 0.11020774 0.10095889 0.13460894
[17] 0.12256326 0.16325352 0.13366212 0.12280966 0.09710267 0.09389212 0.07589208 0.10339667
[25] 0.09201891 0.10769727 0.09610167 0.06800812 0.09091154 0.08692299 0.08550895 0.10504501
[33] 0.11432958 0.10362410 0.07948290 0.10897734

[[6]][[2]]$y
 [1] 0.04406408 0.13661181 0.06293692 0.02597394 0.07365702 0.03822742 0.09246097 0.06132521
 [9] 0.17521642 0.07087068 0.06876656 0.04545737 0.03235644 0.12705362 0.08744182 0.18482501
[17] 0.12382793 0.21023192 0.14893955 0.14976532 0.09409409 0.06222172 0.05386229 0.09101813
[25] 0.07425352 0.12358736 0.09018412 0.06296215 0.06940291 0.06725038 0.07742249 0.12659250
[33] 0.12924799 0.13068753 0.05722104 0.13077936

[[6]][[2]]$yf
 [1] 0.05207970 0.12854851 0.05207970 0.05207970 0.07072553 0.05207970 0.09125375 0.05207970
 [9] 0.18002072 0.07072553 0.05207970 0.05207970 0.03235644 0.12854851 0.09125375 0.18002072
[17] 0.12854851 0.21023192 0.14935244 0.14935244 0.09125375 0.07072553 0.05207970 0.09125375
[25] 0.07072553 0.12854851 0.09018412 0.05207970 0.07072553 0.07072553 0.07072553 0.12854851
[33] 0.12854851 0.12854851 0.05207970 0.12854851


[[6]][[3]]


[[7]]
[[7]][[1]]
$sites
               PCoA1        PCoA2
FRP_1_1  0.018644224  0.050111296
FRP_1_2 -0.116287721  0.026197492
FRP_1_3 -0.022436272  0.039460893
FRP_2_1 -0.086938562 -0.057004098
FRP_2_2 -0.006337469 -0.015211065
FRP_2_3  0.039072086 -0.021516388
FRP_3_1  0.037057588 -0.010721903
FRP_3_2  0.060726713 -0.003104382
FRP_3_3  0.076499412 -0.008211845

$centroids
         PCoA1        PCoA2
1 -0.028483792  0.039471876
2 -0.006610574 -0.018272896
3  0.061086054 -0.007061574

attr(,"class")
[1] "ordiplot"

[[7]][[2]]
[[7]][[2]]$x
 [1] 0.15408060 0.09098169 0.15403651 0.09542980 0.10571582 0.09943907 0.08278124 0.10682108
 [9] 0.11057966 0.10751800 0.12893625 0.16836227 0.16625181 0.18510476 0.19938865 0.12828454
[17] 0.08236546 0.10880524 0.09870944 0.10932608 0.11684214 0.11152001 0.15047559 0.14527013
[25] 0.16122280 0.17699655 0.06838509 0.08789122 0.08882719 0.10182858 0.08537543 0.06656415
[33] 0.07512382 0.06827236 0.06488493 0.05333727

[[7]][[2]]$y
 [1] 0.23580584 0.08657349 0.23432661 0.09129396 0.11079032 0.07513840 0.06039865 0.10898145
 [9] 0.15421236 0.11537462 0.19294183 0.25356560 0.23723003 0.26836012 0.29742812 0.15111241
[17] 0.05517059 0.11551657 0.08894267 0.11461235 0.14881890 0.15469619 0.19851028 0.19904974
[25] 0.24015551 0.25088354 0.06261595 0.04618270 0.08553814 0.10490566 0.03625415 0.06631601
[33] 0.05324613 0.04278573 0.06048318 0.04871463

[[7]][[2]]$yf
 [1] 0.23580584 0.08549733 0.23432661 0.08549733 0.10988588 0.08549733 0.05371701 0.10988588
 [9] 0.15220997 0.11516785 0.19294183 0.25222457 0.23869277 0.26836012 0.29742812 0.15220997
[17] 0.05371701 0.11516785 0.08549733 0.11516785 0.15220997 0.15220997 0.19878001 0.19878001
[25] 0.23869277 0.25222457 0.05371701 0.05371701 0.08549733 0.10490566 0.05371701 0.05371701
[33] 0.05371701 0.05371701 0.05371701 0.04871463


[[7]][[3]]


[[8]]
[[8]][[1]]
$sites
              PCoA1        PCoA2
FRP_1_1  0.05330609 -0.031014795
FRP_1_2  0.05474506 -0.020998469
FRP_1_3  0.02379525 -0.043544199
FRP_2_1  0.02893802  0.043458186
FRP_2_2 -0.05393802  0.001767947
FRP_2_3  0.04937047  0.040515655
FRP_3_1 -0.08813066  0.004220599
FRP_3_2 -0.09929917 -0.006695155
FRP_3_3  0.03121296  0.012290231

$centroids
        PCoA1         PCoA2
1  0.04550140 -0.0312197924
2  0.02081394  0.0354897891
3 -0.07486700  0.0009467908

attr(,"class")
[1] "ordiplot"

[[8]][[2]]
[[8]][[2]]$x
 [1] 0.07192330 0.07909866 0.10047336 0.13340879 0.08861081 0.15638693 0.16261143 0.07817981
 [9] 0.08468035 0.09322242 0.13396872 0.09049408 0.15617428 0.16529537 0.08010778 0.09772089
[17] 0.11668041 0.10398264 0.13624896 0.14364076 0.09561981 0.11584932 0.07673165 0.13663881
[25] 0.15200740 0.08272309 0.13466223 0.09774362 0.09384041 0.11724206 0.15361650 0.16253229
[33] 0.07873143 0.07067902 0.13978029 0.14176573

[[8]][[2]]$y
 [1] 8.261376e-07 4.574570e-05 4.103076e-05 1.209939e-01 3.917155e-05 1.210414e-01
 [7] 1.210478e-01 5.337341e-05 4.535812e-05 4.116155e-05 1.209937e-01 3.836345e-05
[13] 1.210412e-01 1.210476e-01 5.266326e-05 2.787889e-05 1.209497e-01 5.104103e-05
[19] 1.209971e-01 1.210036e-01 2.753982e-05 1.209560e-01 6.587051e-05 1.210035e-01
[25] 1.210099e-01 5.379911e-05 1.209926e-01 4.761477e-05 5.389795e-05 1.209566e-01
[31] 1.210400e-01 1.210465e-01 3.596993e-05 7.064322e-06 1.210041e-01 1.210105e-01

[[8]][[2]]$yf
 [1] 3.945230e-06 4.462925e-05 4.462925e-05 1.209934e-01 4.462925e-05 1.210414e-01
 [7] 1.210477e-01 4.462925e-05 4.462925e-05 4.462925e-05 1.209934e-01 4.462925e-05
[13] 1.210412e-01 1.210477e-01 4.462925e-05 4.462925e-05 1.209528e-01 5.104103e-05
[19] 1.209971e-01 1.210070e-01 4.462925e-05 1.209528e-01 4.462925e-05 1.210035e-01
[25] 1.210099e-01 4.462925e-05 1.209934e-01 4.462925e-05 4.462925e-05 1.209566e-01
[31] 1.210400e-01 1.210465e-01 4.462925e-05 3.945230e-06 1.210041e-01 1.210070e-01


[[8]][[3]]


[[9]]
[[9]][[1]]
$sites
               PCoA1         PCoA2
FRP_2_2 -0.012903642  0.0033319266
FRP_1_1 -0.024343127  0.0059714816
FRP_2_3  0.005336265 -0.0063422706
FRP_1_2  0.030020546  0.0093749670
FRP_1_3  0.002556233 -0.0035074582
FRP_3_3  0.011697789 -0.0112489763
FRP_3_1  0.019047681  0.0032600475
FRP_2_1 -0.012233598  0.0004484654
FRP_3_2 -0.019178147 -0.0012881829

$centroids
         PCoA1         PCoA2
1  0.002556233 -0.0035074542
2 -0.010207025  0.0008571281
3  0.009758724 -0.0052784397

attr(,"class")
[1] "ordiplot"

[[9]][[2]]
[[9]][[2]]$x
 [1] 0.012249502 0.022377459 0.043543925 0.017289068 0.028541047 0.032797207 0.009234898
 [8] 0.015103742 0.034245755 0.055398344 0.028871185 0.040328636 0.044595792 0.020421552
[15] 0.019143236 0.030282660 0.009063522 0.015379388 0.019250908 0.023057360 0.026724602
[22] 0.030388353 0.028798673 0.016001443 0.044216609 0.051210767 0.012225053 0.019307238
[29] 0.017510125 0.024672870 0.018954241 0.029157544 0.036132457 0.033359628 0.040166419
[36] 0.015377484

[[9]][[2]]$y
 [1] 2.728459e-02 2.729928e-02 7.463239e-02 2.729609e-02 5.272559e-02 5.274842e-02
 [7] 1.915832e-05 2.728667e-02 5.277094e-02 1.019168e-01 5.276588e-02 7.463815e-02
[13] 7.944511e-02 2.728618e-02 2.729432e-02 5.275088e-02 8.324205e-06 2.729816e-02
[19] 2.729797e-02 2.730735e-02 3.871991e-02 5.275856e-02 5.271996e-02 2.729788e-02
[25] 7.463072e-02 9.147078e-02 2.729708e-02 2.730457e-02 2.730416e-02 3.871223e-02
[31] 2.729785e-02 5.273789e-02 5.286928e-02 5.275173e-02 6.547738e-02 2.730400e-02

[[9]][[2]]$yf
 [1] 2.728945e-02 2.729928e-02 7.463375e-02 2.729812e-02 5.272277e-02 5.275291e-02
 [7] 1.915832e-05 2.728945e-02 5.277094e-02 1.019168e-01 5.275155e-02 7.463375e-02
[13] 7.944511e-02 2.729812e-02 2.729812e-02 5.275155e-02 8.324205e-06 2.729812e-02
[19] 2.729812e-02 2.730735e-02 3.871991e-02 5.275291e-02 5.272277e-02 2.729812e-02
[25] 7.463375e-02 9.147078e-02 2.728945e-02 2.729812e-02 2.729812e-02 3.871223e-02
[31] 2.729812e-02 5.275155e-02 5.286928e-02 5.275291e-02 6.547738e-02 2.729812e-02


[[9]][[3]]


[[10]]
[[10]][[1]]
$sites
             PCoA1         PCoA2
FRP_2_3 -0.1129215 -0.0235242886
FRP_3_1 -0.1085090 -0.0926596305
FRP_3_2 -0.1109232 -0.0673314110
FRP_1_1 -0.1098511  0.0698295568
FRP_2_1 -0.1119639 -0.0485883296
FRP_1_2  0.8862394 -0.0004000677
FRP_1_3 -0.1061476  0.1144883837
FRP_2_2 -0.1127645  0.0283004742
FRP_3_3 -0.1131584  0.0198853127

$centroids
        PCoA1       PCoA2
1 -0.08319139  0.08974263
2 -0.11279088 -0.02261110
3 -0.11073208 -0.06478154

attr(,"class")
[1] "ordiplot"

[[10]][[2]]
[[10]][[2]]$x
 [1] 0.07896193 0.05253035 0.10571999 0.03899107 0.99966198 0.14311035 0.06060667 0.04814131
 [9] 0.04684927 0.16923263 0.06024814 0.99929467 0.21088097 0.12436663 0.11177748 0.14665749
[17] 0.03386601 0.99963411 0.18446158 0.10154417 0.08907881 0.12689191 0.99933964 0.08634292
[25] 0.05661381 0.05757869 0.99957339 0.16830648 0.08179215 0.06931322 0.99960286 0.99958696
[33] 0.99946317 0.09801482 0.09910349 0.01258915

[[10]][[2]]$y
 [1]   0.20470314   0.11008698   0.20874640   0.10011176 877.11779827   0.25472219
 [7]   0.17229728   0.15213436   0.09811550   0.27366930   0.10721820 877.00438316
[13]   0.18342433   0.28515148   0.26617767   0.24072377   0.03671387 877.07350870
[19]   0.21247561   0.23115184   0.20996577   0.20415966 876.93104898   0.15492892
[25]   0.06157179   0.06856141 877.04939491   0.18344158   0.19694596   0.17602868
[31] 876.86766147 876.98890678 876.99956613   0.20269417   0.19516103   0.02143671

[[10]][[2]]$yf
 [1]   0.18552601   0.09843030   0.21994912   0.09843030 877.11779827   0.23377173
 [7]   0.17229728   0.09843030   0.09843030   0.23377173   0.10721820 876.96771607
[13]   0.23377173   0.23377173   0.23377173   0.23377173   0.03671387 877.07350870
[19]   0.23377173   0.21994912   0.20260699   0.23377173 876.96771607   0.18552601
[25]   0.09843030   0.09843030 876.97638232   0.23377173   0.18552601   0.17602868
[31] 876.97638232 876.97638232 876.97638232   0.20260699   0.20260699   0.02143671


[[10]][[3]]


[[11]]
[[11]][[1]]
$sites
              PCoA1       PCoA2
FRP_1_1 -0.09400627 -0.01329871
FRP_1_2 -0.06080563  0.02983990
FRP_1_3 -0.04081372 -0.02127699
FRP_2_1 -0.01763770 -0.02653275
FRP_2_2 -0.03687852  0.04266341
FRP_2_3  0.02357176 -0.02655387
FRP_3_1  0.24198995  0.02217142
FRP_3_2  0.04193813 -0.04371059
FRP_3_3 -0.05735799  0.03669819

$centroids
         PCoA1        PCoA2
1 -0.063749272  0.005398960
2 -0.007845245 -0.007760707
3  0.044110954 -0.034511892

attr(,"class")
[1] "ordiplot"

[[11]][[2]]
[[11]][[2]]$x
 [1] 0.08867492 0.11118395 0.12315747 0.12310010 0.15366852 0.34104496 0.15739338 0.10813631
 [9] 0.08453847 0.09753411 0.09124153 0.12871589 0.30515101 0.14431388 0.07744923 0.09428018
[17] 0.12176223 0.11167290 0.29214634 0.13183991 0.10471197 0.10926224 0.09295979 0.27135258
[25] 0.10324325 0.10429229 0.10925194 0.29048895 0.13376635 0.10122935 0.23573331 0.08476898
[33] 0.13061640 0.21948618 0.30571728 0.14301322

[[11]][[2]]$y
 [1] 2.309236e-04 4.449857e-04 5.131447e-04 3.991991e-04 6.801282e-04 3.832354e-01
 [7] 8.223628e-04 2.334615e-04 2.490000e-04 2.824557e-04 2.563295e-04 4.653311e-04
[13] 3.830136e-01 5.930522e-04 2.161538e-05 2.162621e-04 4.240885e-04 4.476692e-04
[19] 3.828902e-01 4.815950e-04 2.333546e-04 2.966127e-04 2.322963e-04 3.827381e-01
[25] 3.122568e-04 2.830543e-04 3.318049e-04 3.828625e-01 5.245366e-04 2.762156e-04
[31] 3.825554e-01 2.101918e-04 4.739155e-04 3.824267e-01 3.830182e-01 5.949130e-04

[[11]][[2]]$yf
 [1] 2.309236e-04 4.289856e-04 4.834966e-04 4.289856e-04 6.801282e-04 3.832354e-01
 [7] 8.223628e-04 2.701331e-04 2.295959e-04 2.701331e-04 2.349626e-04 4.834966e-04
[13] 3.830136e-01 5.939826e-04 2.161538e-05 2.349626e-04 4.289856e-04 4.289856e-04
[19] 3.828902e-01 4.834966e-04 2.701331e-04 3.142088e-04 2.349626e-04 3.827381e-01
[25] 2.701331e-04 2.701331e-04 3.142088e-04 3.828625e-01 5.245366e-04 2.701331e-04
[31] 3.825554e-01 2.295959e-04 4.834966e-04 3.824267e-01 3.830182e-01 5.939826e-04


[[11]][[3]]


[[12]]
[[12]][[1]]
$sites
              PCoA1        PCoA2
FRP_1_1  0.13633452  0.007020356
FRP_1_2 -0.07427683  0.090627628
FRP_1_3 -0.23293488 -0.063555514
FRP_2_1 -0.16906896  0.065042378
FRP_2_2 -0.21907658 -0.044549303
FRP_2_3  0.12276620 -0.005723485
FRP_3_1  0.15730028 -0.013551720
FRP_3_2  0.13831976 -0.003159585
FRP_3_3  0.14063649 -0.032150755

$centroids
        PCoA1       PCoA2
1 -0.07020373  0.06086299
2 -0.15374948  0.02949032
3  0.14523099 -0.01419899

attr(,"class")
[1] "ordiplot"

[[12]][[2]]
[[12]][[2]]$x
 [1] 0.25230432 0.38295668 0.32072753 0.37381292 0.10645175 0.11229274 0.09999688 0.13304752
 [9] 0.22984910 0.15226335 0.21872760 0.23731514 0.27341607 0.25047448 0.25930873 0.17510279
[17] 0.11102898 0.36952033 0.40401055 0.38735462 0.39142903 0.13477951 0.31294109 0.34483294
[25] 0.32547392 0.34271947 0.35483586 0.38726032 0.36575812 0.37086130 0.10867488 0.09517648
[33] 0.12418441 0.10466003 0.13073032 0.12089383

[[12]][[2]]$y
 [1] 0.3543938762 0.6082126426 0.3648138016 0.6079327052 0.0003874823 0.0004683584
 [7] 0.0002460423 0.0007476549 0.3479555703 0.2710460504 0.3479340104 0.3540767465
[13] 0.3545840778 0.3543277032 0.3542058701 0.2710467481 0.0005179020 0.6080475045
[19] 0.6085898312 0.6082725608 0.6084076124 0.2706360709 0.3647420805 0.3652486332
[25] 0.3649317535 0.3651839900 0.6077678185 0.6083100927 0.6079927945 0.6081281924
[31] 0.0005472217 0.0002513606 0.0005171008 0.0003196526 0.0004802306 0.0005016682

[[12]][[2]]$yf
 [1] 0.3543091498 0.6082126426 0.3648138016 0.6080361340 0.0003874823 0.0005054136
 [7] 0.0002487015 0.0007476549 0.3479555703 0.2710460504 0.3479340104 0.3540767465
[13] 0.3545840778 0.3543091498 0.3543091498 0.2710467481 0.0005054136 0.6080361340
[19] 0.6085898312 0.6082913268 0.6084076124 0.2706360709 0.3647420805 0.3652486332
[25] 0.3649317535 0.3651839900 0.6077678185 0.6082913268 0.6079927945 0.6080361340
[31] 0.0005054136 0.0002487015 0.0005054136 0.0003196526 0.0005054136 0.0005054136


[[12]][[3]]


[[13]]
[[13]][[1]]
$sites
               PCoA1        PCoA2
FRP_1_1 -0.040933368  0.012037860
FRP_1_2 -0.035049645  0.012805583
FRP_1_3 -0.034235234 -0.003442305
FRP_2_1  0.009620739 -0.008295548
FRP_2_2  0.014359868 -0.037189729
FRP_2_3 -0.001289886 -0.018053451
FRP_3_1  0.032747273  0.010376822
FRP_3_2  0.021816734 -0.002470293
FRP_3_3  0.032963520  0.034231061

$centroids
         PCoA1        PCoA2
1 -0.036662371  0.007679577
2  0.007709566 -0.021308398
3  0.029977051  0.013699546

attr(,"class")
[1] "ordiplot"

[[13]][[2]]
[[13]][[2]]$x
 [1] 0.06104226 0.06856393 0.07932263 0.08413225 0.07064816 0.08777414 0.08625987 0.08962218
 [9] 0.06278358 0.07392153 0.08053554 0.07351484 0.07914690 0.08348338 0.08754436 0.06986980
[17] 0.07872013 0.07399851 0.08708987 0.08156579 0.08844205 0.06143118 0.06311144 0.06876200
[25] 0.06970861 0.06539897 0.06259994 0.06512319 0.07278045 0.08014720 0.07034222 0.07493446
[33] 0.07586844 0.06298123 0.05993611 0.07687521

[[13]][[2]]$y
 [1] 0.01606697 0.02518159 0.04660328 0.04559271 0.03958380 0.06653044 0.05910220 0.07995054
 [9] 0.01113316 0.03724560 0.04033046 0.03773078 0.05476687 0.04406416 0.06982057 0.04222320
[17] 0.04781195 0.04687470 0.05656817 0.04144700 0.07278461 0.01218069 0.02037843 0.02134685
[25] 0.02845840 0.03335028 0.00988722 0.03035252 0.04063731 0.03767527 0.04008920 0.04801302
[33] 0.04730013 0.02332879 0.01707774 0.03986392

[[13]][[2]]$yf
 [1] 0.01326916 0.02755781 0.04497734 0.04559271 0.03958498 0.06817551 0.05783518 0.07995054
 [9] 0.01326916 0.03958498 0.04497734 0.03958498 0.04497734 0.04497734 0.06817551 0.03958498
[17] 0.04497734 0.04497734 0.05783518 0.04497734 0.07278461 0.01326916 0.02185361 0.02755781
[25] 0.02845840 0.02755781 0.01326916 0.02755781 0.03958498 0.04497734 0.03958498 0.04497734
[33] 0.04497734 0.02185361 0.01326916 0.04497734


[[13]][[3]]


[[14]]
[[14]][[1]]
$sites
               PCoA1        PCoA2
FRP_2_2  0.043097350  0.021621098
FRP_1_1 -0.039971382  0.015904363
FRP_1_2  0.024933783 -0.008642039
FRP_1_3  0.006557278 -0.019743956
FRP_2_1  0.011226499  0.001345905
FRP_2_3  0.012856685  0.015191099
FRP_3_2 -0.030369094  0.007631092
FRP_3_3  0.009631459 -0.025092552
FRP_3_1 -0.037962578 -0.008215009

$centroids
         PCoA1        PCoA2
1  0.004484296 -0.010747992
2  0.017641163  0.011911074
3 -0.025621439 -0.004390609

attr(,"class")
[1] "ordiplot"

[[14]][[2]]
[[14]][[2]]$x
 [1] 0.08574554 0.04431149 0.06150028 0.05317334 0.04728536 0.07875579 0.06075227 0.08845123
 [9] 0.07293810 0.06312346 0.06032895 0.06235418 0.03453591 0.06897412 0.03428400 0.03970183
[17] 0.04228929 0.04262655 0.06631820 0.03910728 0.06630515 0.03729165 0.04398514 0.05495980
[25] 0.03380931 0.05392512 0.03060442 0.05548489 0.04121477 0.06001058 0.05131472 0.05054695
[33] 0.06248243 0.05472383 0.03510436 0.05745512

[[14]][[2]]$y
 [1] 0.131068524 0.052617133 0.075554514 0.055900369 0.053004285 0.111206145 0.078647151
 [8] 0.125564316 0.102483308 0.075941772 0.076308198 0.078227421 0.020736204 0.081617308
[15] 0.025353823 0.029283057 0.035447329 0.044852734 0.081921082 0.028754344 0.088352404
[22] 0.031105238 0.043023956 0.056128657 0.008268931 0.059556324 0.011996140 0.055913675
[29] 0.038489753 0.069742675 0.058810100 0.050482755 0.075441598 0.062385694 0.022242465
[36] 0.063442404

[[14]][[2]]$yf
 [1] 0.12831642 0.05203472 0.07676249 0.05735523 0.05203472 0.11120614 0.07676249 0.12831642
 [9] 0.10248331 0.07676249 0.07630820 0.07676249 0.02277750 0.08396360 0.02277750 0.02971421
[17] 0.03696854 0.04393834 0.08396360 0.02971421 0.08396360 0.02971421 0.04393834 0.05849609
[25] 0.01013254 0.05849609 0.01013254 0.05849609 0.03696854 0.06974268 0.05735523 0.05203472
[33] 0.07676249 0.05849609 0.02277750 0.06344240


[[14]][[3]]


[[15]]
[[15]][[1]]
$sites
              PCoA1         PCoA2
FRP_1_1 -0.02456990 -0.0078054647
FRP_1_2 -0.06012271 -0.0035496882
FRP_1_3 -0.03971974  0.0009540191
FRP_2_1  0.03998716 -0.0309370731
FRP_2_2  0.03188282 -0.0042321271
FRP_2_3  0.01937631 -0.0483915539
FRP_3_1 -0.02026605  0.0127691874
FRP_3_2  0.02771215  0.0566577272
FRP_3_3  0.02571995  0.0245349733

$centroids
        PCoA1        PCoA2
1 -0.04139507 -0.002919834
2  0.03182273 -0.029372792
3  0.01090157  0.030844533

attr(,"class")
[1] "ordiplot"

[[15]][[2]]
[[15]][[2]]$x
 [1] 0.08627085 0.07467077 0.09069655 0.09513708 0.09352712 0.07587892 0.10805343 0.09550277
 [9] 0.07349903 0.11643696 0.10814451 0.10779682 0.08859526 0.12135347 0.11213361 0.10300098
[17] 0.10276712 0.08966838 0.07844306 0.10174117 0.10139020 0.07714854 0.06936040 0.09424953
[25] 0.10131648 0.09631371 0.09041941 0.08726381 0.10165937 0.08276320 0.10290547 0.11187175
[33] 0.10304963 0.10068219 0.09694484 0.09950881

[[15]][[2]]$y
 [1] 0.04834254 0.02161578 0.05058223 0.05466773 0.04786761 0.02162042 0.07044269 0.05873546
 [9] 0.02714228 0.09572114 0.10289209 0.08044237 0.05554656 0.10162854 0.10509404 0.07119872
[17] 0.07626376 0.06205428 0.03039378 0.07982009 0.07812098 0.02202406 0.03157749 0.06187510
[25] 0.08873590 0.04801430 0.05239793 0.05800210 0.07212595 0.02743176 0.06730121 0.10770321
[33] 0.07494797 0.05043938 0.05148136 0.04694849

[[15]][[2]]$yf
 [1] 0.04834254 0.02479601 0.05373942 0.05373942 0.05373942 0.02479601 0.07593996 0.05373942
 [9] 0.02479601 0.10260780 0.10260780 0.07593996 0.05373942 0.10260780 0.10260780 0.07593996
[17] 0.07593996 0.05373942 0.02891277 0.07593996 0.07593996 0.02479601 0.02479601 0.05373942
[25] 0.07593996 0.05373942 0.05373942 0.05373942 0.07593996 0.02891277 0.07593996 0.10260780
[33] 0.07593996 0.05373942 0.05373942 0.05373942


[[15]][[3]]


[[16]]
[[16]][[1]]
$sites
             PCoA1         PCoA2
FRP_1_2 -0.4565473 -0.0009434912
FRP_2_1 -0.4481572 -0.0033794703
FRP_1_1  0.3647707 -0.1605863750
FRP_1_3 -0.4735575 -0.0020271124
FRP_2_2 -0.4540831  0.0008995818
FRP_3_1  0.3437789  0.1997244792
FRP_3_3  0.3741651 -0.0859375311
FRP_2_3  0.3722042  0.0280109316
FRP_3_2  0.3774263  0.0242389874

$centroids
       PCoA1         PCoA2
1 -0.4457850 -0.0043218452
2 -0.4284775 -0.0006543993
3  0.3774263  0.0242390033

attr(,"class")
[1] "ordiplot"

[[16]][[2]]
[[16]][[2]]$x
 [1] 0.12959188 0.84032087 0.06865736 0.11057519 0.82838352 0.83890884 0.83388625 0.83815497
 [9] 0.83269335 0.13069629 0.07872825 0.82198437 0.83153749 0.82598902 0.83126876 0.85680253
[17] 0.83781769 0.36220241 0.11457519 0.20839526 0.20070079 0.11483284 0.84493338 0.85537177
[25] 0.85074094 0.85566454 0.82528251 0.83667436 0.83090591 0.83559903 0.29374275 0.19503828
[33] 0.19595278 0.13939317 0.13921123 0.08413552

[[16]][[2]]$y
 [1]   0.25447710 565.62302200   0.21031959   0.12091152 565.40820578 565.59495216
 [7] 565.45730305 565.55112045 565.49797865   0.33685185   0.13742228 565.28299192
[13] 565.46977205 565.33218773 565.42599762 565.81035035 565.54528211   0.48528651
[19]   0.35015389   0.24738371   0.21519273   0.26508507 565.59546051 565.78222148
[25] 565.64460034 565.73841450 565.33039465 565.51715513 565.37953309 565.47334735
[31]   0.20567264   0.25619786   0.27277321   0.21511317   0.15261439   0.09574866

[[16]][[2]]$yf
 [1]   0.2519560 565.6092413   0.1411005   0.1411005 565.3938694 565.5949522 565.4762097
 [8] 565.5511205 565.4762097   0.2519560   0.1411005 565.2829919 565.4697721 565.3321877
[15] 565.4259976 565.8103504 565.5452821   0.4852865   0.2519560   0.2519560   0.2519560
[22]   0.2519560 565.6092413 565.7603180 565.6446003 565.7603180 565.3303947 565.5171551
[29] 565.3938694 565.4762097   0.2519560   0.2519560   0.2519560   0.2519560   0.2519560
[36]   0.1411005


[[16]][[3]]


[[17]]
[[17]][[1]]
$sites
              PCoA1        PCoA2
FRP_1_1  0.01317558  0.057018703
FRP_1_2 -0.14263115  0.034215725
FRP_1_3 -0.03390554  0.033936430
FRP_2_1 -0.10294663 -0.078107663
FRP_2_2 -0.01872972 -0.013878459
FRP_2_3  0.06794507 -0.025960404
FRP_3_1  0.02757863  0.001359694
FRP_3_2  0.07424929  0.007446930
FRP_3_3  0.11526447 -0.016030957

$centroids
        PCoA1        PCoA2
1 -0.04205007  0.038135972
2 -0.01872970 -0.013878539
3  0.07434876  0.003617549

attr(,"class")
[1] "ordiplot"

[[17]][[2]]
[[17]][[2]]$x
 [1] 0.18840692 0.11562999 0.18314765 0.10093731 0.12583074 0.10582942 0.11015630 0.15834665
 [9] 0.13306012 0.13981477 0.14184660 0.22532892 0.18971964 0.22203512 0.26560511 0.14742165
[17] 0.09537047 0.13504411 0.11900675 0.13569655 0.16460378 0.11721231 0.18754497 0.16595795
[25] 0.20236074 0.23481570 0.09758637 0.08891775 0.10698964 0.14377495 0.10401717 0.06297104
[33] 0.07524520 0.07969613 0.11864910 0.06970581

[[17]][[2]]$y
 [1] 0.32196494 0.20006260 0.22088137 0.11168194 0.17236386 0.07804538 0.16834946 0.24901440
 [9] 0.17278395 0.17503967 0.23290982 0.33689371 0.32122760 0.34622992 0.41847056 0.20807817
[17] 0.08866121 0.16447658 0.16737690 0.17425771 0.24627094 0.19461203 0.32480315 0.26204863
[25] 0.32887516 0.41598295 0.13021797 0.08832286 0.13476313 0.22140441 0.09448960 0.01224378
[33] 0.09118654 0.09033007 0.17300189 0.08792388

[[17]][[2]]$yf
 [1] 0.32266523 0.17710835 0.24455384 0.10360872 0.17710835 0.10360872 0.16834946 0.24455384
 [9] 0.17710835 0.17710835 0.22079747 0.34156182 0.32266523 0.34156182 0.41847056 0.22079747
[17] 0.08962517 0.17710835 0.17710835 0.17710835 0.24455384 0.17710835 0.32266523 0.24455384
[25] 0.32887516 0.41598295 0.10360872 0.08962517 0.13476313 0.22079747 0.10360872 0.01224378
[33] 0.08962517 0.08962517 0.17710835 0.08792388


[[17]][[3]]


[[18]]
[[18]][[1]]
$sites
               PCoA1        PCoA2
FRP_3_1  0.105596144 -0.021325568
FRP_1_1 -0.066600410  0.027909600
FRP_1_2 -0.035287019 -0.020264373
FRP_1_3 -0.019748002 -0.062198954
FRP_2_1 -0.003049028 -0.058744369
FRP_2_2 -0.004816502  0.056526821
FRP_2_3  0.023839836  0.008949593
FRP_3_2  0.031377266  0.067192442
FRP_3_3 -0.031312285  0.001954807

$centroids
        PCoA1        PCoA2
1 -0.03716566 -0.020070974
2  0.01448872  0.006329528
3  0.03059691  0.023254901

attr(,"class")
[1] "ordiplot"

[[18]][[2]]
[[18]][[2]]$x
 [1] 0.18219357 0.14318786 0.13945648 0.13659006 0.14024335 0.10839739 0.13291422 0.14763386
 [9] 0.07405135 0.11034382 0.12075680 0.08545951 0.11037669 0.11573331 0.08106146 0.06739269
[17] 0.08759362 0.08898974 0.08594184 0.12879086 0.05293174 0.05323006 0.12270565 0.10126061
[25] 0.14416067 0.09031536 0.13154407 0.09007812 0.13120021 0.10433042 0.08416310 0.06624057
[33] 0.08304585 0.07719591 0.07516047 0.11677145

[[18]][[2]]$y
 [1] 0.292321175 0.226235208 0.214118034 0.166656620 0.221601343 0.141459807 0.167920077
 [8] 0.232720252 0.086992115 0.164492218 0.179953640 0.090194696 0.151060055 0.176201841
[15] 0.078998826 0.081099750 0.093279843 0.098014528 0.090818034 0.161172184 0.008120363
[22] 0.047472319 0.171260695 0.119049074 0.212556176 0.087989802 0.161531264 0.087693041
[29] 0.183799799 0.101390953 0.092225149 0.086069432 0.095224136 0.096136261 0.095814125
[36] 0.162019852

[[18]][[2]]$yf
 [1] 0.292321175 0.220130909 0.214118034 0.170327754 0.220130909 0.141459807 0.170327754
 [8] 0.232720252 0.086992115 0.157776136 0.170327754 0.091929904 0.157776136 0.169110846
[15] 0.090316404 0.083584591 0.091929904 0.091929904 0.091929904 0.170327754 0.008120363
[22] 0.047472319 0.170327754 0.110220014 0.220130909 0.091929904 0.170327754 0.091929904
[29] 0.170327754 0.110220014 0.091929904 0.083584591 0.091929904 0.090316404 0.090316404
[36] 0.169110846


[[18]][[3]]


[[19]]
[[19]][[1]]
$sites
                PCoA1         PCoA2
FRP_1_2  0.0444601405 -0.0216096941
FRP_3_3 -0.0453399997 -0.0289116660
FRP_3_2  0.0464638373 -0.0159208413
FRP_2_2 -0.0458488432  0.0053054021
FRP_2_3  0.0104043911  0.0252458669
FRP_3_1  0.0138771942 -0.0003034433
FRP_2_1  0.0003415477  0.0221493374
FRP_1_3  0.0172867403  0.0161506964
FRP_1_1 -0.0416450082 -0.0021056581

$centroids
         PCoA1        PCoA2
1  0.014388335  0.007896744
2 -0.002599866  0.020936118
3  0.013764139 -0.003511919

attr(,"class")
[1] "ordiplot"

[[19]][[2]]
[[19]][[2]]$x
 [1] 0.09085869 0.02337141 0.09596493 0.06028502 0.03889996 0.06529771 0.05066655 0.09034789
 [9] 0.09476172 0.04362363 0.07917507 0.07132417 0.07045267 0.07934011 0.03140956 0.09718028
[17] 0.06027608 0.04098046 0.06266884 0.04832538 0.08982244 0.06648336 0.05948141 0.05625081
[25] 0.06875000 0.02535126 0.03899505 0.03009547 0.03077166 0.06273180 0.03463583 0.02995577
[33] 0.05810217 0.03097032 0.05215542 0.06427192

[[19]][[2]]$y
 [1] 0.1586431318 0.0001806508 0.1583971202 0.1051713312 0.0572636238 0.1054668710
 [7] 0.0744532133 0.1411175284 0.1586507719 0.0568496262 0.1428856761 0.1197218818
[13] 0.1127601933 0.1398781910 0.0408002278 0.1583405856 0.1050160004 0.0571559946
[19] 0.1053441744 0.0742976827 0.1410808403 0.1050082793 0.1056065084 0.0762998208
[25] 0.1135058135 0.0242331322 0.0568045398 0.0302394679 0.0307188213 0.1046347978
[31] 0.0489248604 0.0310279693 0.0923707704 0.0402449081 0.0744277209 0.1063791965

[[19]][[2]]$yf
 [1] 0.1585079024 0.0001806508 0.1585079024 0.1051545625 0.0570184461 0.1056181156
 [7] 0.0744404671 0.1412405589 0.1585079024 0.0570184461 0.1412405589 0.1197218818
[13] 0.1131330034 0.1412405589 0.0408002278 0.1585079024 0.1051545625 0.0570184461
[19] 0.1051545625 0.0742976827 0.1412405589 0.1056181156 0.1051545625 0.0762998208
[25] 0.1131330034 0.0242331322 0.0570184461 0.0306337186 0.0307188213 0.1051545625
[31] 0.0489248604 0.0306337186 0.0923707704 0.0402449081 0.0744404671 0.1056181156


[[19]][[3]]

Vouchered Reference dataframe

Here, I’m using a loc list that doesn’t include 16Sfish and crust2 because they have too few samples to include.

# cycle over the list of loci for the full reference pool sample replicates
# using the bray-curtis function to test for dissimilarity
# two of the loci were removed because they had too little data remaining after the sodm filter step
lapply(loc_list19, bray_nmds_complete, sodm_filtered_df = vrp_sodm_filtered_df, sample = "VRP")
Run 0 stress 0 
Run 1 stress 0 
... Procrustes: rmse 0.2188576  max resid 0.4546289 
Run 2 stress 0 
... Procrustes: rmse 0.1629029  max resid 0.3723626 
Run 3 stress 0 
... Procrustes: rmse 0.2600044  max resid 0.5112368 
Run 4 stress 0 
... Procrustes: rmse 0.1920451  max resid 0.3739882 
Run 5 stress 0 
... Procrustes: rmse 0.1419563  max resid 0.319324 
Run 6 stress 0 
... Procrustes: rmse 0.1375993  max resid 0.2651579 
Run 7 stress 0 
... Procrustes: rmse 0.164848  max resid 0.3344819 
Run 8 stress 0 
... Procrustes: rmse 0.162067  max resid 0.2551065 
Run 9 stress 0 
... Procrustes: rmse 0.1838458  max resid 0.4614907 
Run 10 stress 0 
... Procrustes: rmse 0.1531954  max resid 0.3104926 
Run 11 stress 0 
... Procrustes: rmse 0.09379692  max resid 0.1764086 
Run 12 stress 0 
... Procrustes: rmse 0.2336251  max resid 0.5324595 
Run 13 stress 0 
... Procrustes: rmse 0.2495365  max resid 0.455896 
Run 14 stress 0 
... Procrustes: rmse 0.2658785  max resid 0.4391367 
Run 15 stress 0 
... Procrustes: rmse 0.2080438  max resid 0.4265525 
Run 16 stress 0 
... Procrustes: rmse 0.1905128  max resid 0.3659933 
Run 17 stress 0 
... Procrustes: rmse 0.2073191  max resid 0.4117981 
Run 18 stress 0 
... Procrustes: rmse 0.198308  max resid 0.4213292 
Run 19 stress 0 
... Procrustes: rmse 0.2051783  max resid 0.4216974 
Run 20 stress 0 
... Procrustes: rmse 0.1355869  max resid 0.3115212 
Run 21 stress 0 
... Procrustes: rmse 0.195923  max resid 0.3282201 
Run 22 stress 0 
... Procrustes: rmse 0.1724445  max resid 0.3703548 
Run 23 stress 0 
... Procrustes: rmse 0.1269243  max resid 0.2568244 
Run 24 stress 0 
... Procrustes: rmse 0.2256089  max resid 0.4080003 
Run 25 stress 0 
... Procrustes: rmse 0.08165474  max resid 0.1588491 
Run 26 stress 0 
... Procrustes: rmse 0.1797413  max resid 0.3708846 
Run 27 stress 0 
... Procrustes: rmse 0.0983635  max resid 0.1810968 
Run 28 stress 0 
... Procrustes: rmse 0.1301974  max resid 0.2868027 
Run 29 stress 0 
... Procrustes: rmse 0.1944609  max resid 0.3642681 
Run 30 stress 0 
... Procrustes: rmse 0.2436758  max resid 0.4675065 
Run 31 stress 0 
... Procrustes: rmse 0.1974465  max resid 0.5133868 
Run 32 stress 0 
... Procrustes: rmse 0.2363754  max resid 0.3267545 
Run 33 stress 0 
... Procrustes: rmse 0.2146592  max resid 0.3925539 
Run 34 stress 0 
... Procrustes: rmse 0.2075408  max resid 0.4523453 
Run 35 stress 0 
... Procrustes: rmse 0.1653941  max resid 0.2666775 
Run 36 stress 0 
... Procrustes: rmse 0.1317495  max resid 0.2416324 
Run 37 stress 0 
... Procrustes: rmse 0.1682703  max resid 0.3440028 
Run 38 stress 0 
... Procrustes: rmse 0.08457228  max resid 0.1493885 
Run 39 stress 1.30749e-06 
... Procrustes: rmse 0.2471044  max resid 0.6337704 
Run 40 stress 0 
... Procrustes: rmse 0.1091712  max resid 0.1842388 
Run 41 stress 0 
... Procrustes: rmse 0.1468511  max resid 0.3256452 
Run 42 stress 0 
... Procrustes: rmse 0.2280831  max resid 0.3475688 
Run 43 stress 0 
... Procrustes: rmse 0.170635  max resid 0.3911123 
Run 44 stress 0 
... Procrustes: rmse 0.2733204  max resid 0.5613543 
Run 45 stress 0 
... Procrustes: rmse 0.1332195  max resid 0.2680989 
Run 46 stress 0 
... Procrustes: rmse 0.1364323  max resid 0.2322551 
Run 47 stress 0 
... Procrustes: rmse 0.1750729  max resid 0.3704281 
Run 48 stress 0 
... Procrustes: rmse 0.2258418  max resid 0.4570286 
Run 49 stress 0 
... Procrustes: rmse 0.2048435  max resid 0.4489906 
Run 50 stress 0 
... Procrustes: rmse 0.2463745  max resid 0.4592324 
*** No convergence -- monoMDS stopping criteria:
    50: stress < smin

Run 0 stress 0.1259422 
Run 1 stress 0.1103133 
... New best solution
... Procrustes: rmse 0.2637142  max resid 0.5224047 
Run 2 stress 0.1416419 
Run 3 stress 0.1259422 
Run 4 stress 0.1036948 
... New best solution
... Procrustes: rmse 0.1513322  max resid 0.2323675 
Run 5 stress 0.1292795 
Run 6 stress 0.1036937 
... New best solution
... Procrustes: rmse 0.001168286  max resid 0.002549205 
... Similar to previous best
Run 7 stress 0.1206489 
Run 8 stress 0.1036958 
... Procrustes: rmse 0.001443218  max resid 0.00314999 
... Similar to previous best
Run 9 stress 0.103697 
... Procrustes: rmse 0.001631093  max resid 0.003551549 
... Similar to previous best
Run 10 stress 0.1036941 
... Procrustes: rmse 0.0002481308  max resid 0.0004712785 
... Similar to previous best
Run 11 stress 0.1206521 
Run 12 stress 0.1036955 
... Procrustes: rmse 0.00117882  max resid 0.002568815 
... Similar to previous best
Run 13 stress 0.1259422 
Run 14 stress 0.1259424 
Run 15 stress 0.1259422 
Run 16 stress 0.2803009 
Run 17 stress 0.1259422 
Run 18 stress 0.1206492 
Run 19 stress 0.1259422 
Run 20 stress 0.3209239 
*** Solution reached

Run 0 stress 0.03964791 
Run 1 stress 0.04315421 
Run 2 stress 0.03964791 
... Procrustes: rmse 1.980161e-05  max resid 2.832945e-05 
... Similar to previous best
Run 3 stress 0.03964791 
... Procrustes: rmse 2.805544e-05  max resid 4.056985e-05 
... Similar to previous best
Run 4 stress 0.03964791 
... New best solution
... Procrustes: rmse 5.244541e-06  max resid 7.488455e-06 
... Similar to previous best
Run 5 stress 0.1112105 
Run 6 stress 0.111211 
Run 7 stress 0.03964791 
... New best solution
... Procrustes: rmse 1.366879e-06  max resid 2.249539e-06 
... Similar to previous best
Run 8 stress 0.03964791 
... Procrustes: rmse 4.194253e-06  max resid 7.180948e-06 
... Similar to previous best
Run 9 stress 0.1112105 
Run 10 stress 0.04315421 
Run 11 stress 0.1112111 
Run 12 stress 0.1112098 
Run 13 stress 0.03964791 
... Procrustes: rmse 2.337427e-05  max resid 3.664673e-05 
... Similar to previous best
Run 14 stress 0.03964791 
... Procrustes: rmse 3.228929e-06  max resid 4.435384e-06 
... Similar to previous best
Run 15 stress 0.1084866 
Run 16 stress 0.03964791 
... Procrustes: rmse 1.035472e-05  max resid 2.173901e-05 
... Similar to previous best
Run 17 stress 0.1112101 
Run 18 stress 0.03964791 
... Procrustes: rmse 4.697961e-06  max resid 6.970804e-06 
... Similar to previous best
Run 19 stress 0.03964791 
... New best solution
... Procrustes: rmse 4.849198e-06  max resid 7.792353e-06 
... Similar to previous best
Run 20 stress 0.1112105 
*** Solution reached

some squared distances are negative and changed to zero

Run 0 stress 8.667746e-05 
Run 1 stress 9.536068e-05 
... Procrustes: rmse 0.108884  max resid 0.2666471 
Run 2 stress 9.91464e-05 
... Procrustes: rmse 0.09868257  max resid 0.2408404 
Run 3 stress 9.801766e-05 
... Procrustes: rmse 0.1054047  max resid 0.258108 
Run 4 stress 9.225491e-05 
... Procrustes: rmse 0.1115615  max resid 0.2732391 
Run 5 stress 9.936466e-05 
... Procrustes: rmse 0.04523827  max resid 0.1068417 
Run 6 stress 8.641996e-05 
... New best solution
... Procrustes: rmse 0.110557  max resid 0.2707826 
Run 7 stress 9.755808e-05 
... Procrustes: rmse 0.01668631  max resid 0.03539528 
Run 8 stress 9.276799e-05 
... Procrustes: rmse 0.1605222  max resid 0.3273854 
Run 9 stress 7.891082e-05 
... New best solution
... Procrustes: rmse 0.1750057  max resid 0.4082376 
Run 10 stress 9.935081e-05 
... Procrustes: rmse 0.1484668  max resid 0.3602935 
Run 11 stress 9.934168e-05 
... Procrustes: rmse 0.05826092  max resid 0.1413558 
Run 12 stress 9.014264e-05 
... Procrustes: rmse 0.1354521  max resid 0.3280625 
Run 13 stress 9.892543e-05 
... Procrustes: rmse 0.1723239  max resid 0.4220054 
Run 14 stress 9.738839e-05 
... Procrustes: rmse 0.1680317  max resid 0.4113084 
Run 15 stress 9.951748e-05 
... Procrustes: rmse 0.08788538  max resid 0.2067694 
Run 16 stress 9.932458e-05 
... Procrustes: rmse 0.1746533  max resid 0.4277728 
Run 17 stress 9.645076e-05 
... Procrustes: rmse 0.08944167  max resid 0.2181974 
Run 18 stress 9.814548e-05 
... Procrustes: rmse 0.1557908  max resid 0.3798346 
Run 19 stress 9.695131e-05 
... Procrustes: rmse 0.09101006  max resid 0.2221463 
Run 20 stress 9.709462e-05 
... Procrustes: rmse 0.09020712  max resid 0.2180217 
Run 21 stress 9.776125e-05 
... Procrustes: rmse 0.02232116  max resid 0.05260948 
Run 22 stress 9.727769e-05 
... Procrustes: rmse 0.08804021  max resid 0.2124437 
Run 23 stress 9.707723e-05 
... Procrustes: rmse 0.1515489  max resid 0.3686039 
Run 24 stress 9.681252e-05 
... Procrustes: rmse 0.08551088  max resid 0.2086257 
Run 25 stress 9.738063e-05 
... Procrustes: rmse 0.1697696  max resid 0.4156666 
Run 26 stress 9.246671e-05 
... Procrustes: rmse 0.08090248  max resid 0.1917372 
Run 27 stress 9.571305e-05 
... Procrustes: rmse 0.09685932  max resid 0.2345325 
Run 28 stress 9.619452e-05 
... Procrustes: rmse 0.09309699  max resid 0.215885 
Run 29 stress 9.88892e-05 
... Procrustes: rmse 0.0740892  max resid 0.1781816 
Run 30 stress 0.2967445 
Run 31 stress 9.941774e-05 
... Procrustes: rmse 0.03570365  max resid 0.08464137 
Run 32 stress 8.397398e-05 
... Procrustes: rmse 0.05195618  max resid 0.1239748 
Run 33 stress 9.993281e-05 
... Procrustes: rmse 0.172526  max resid 0.4225068 
Run 34 stress 9.789951e-05 
... Procrustes: rmse 0.1715659  max resid 0.4201453 
Run 35 stress 9.174099e-05 
... Procrustes: rmse 0.1475248  max resid 0.3577374 
Run 36 stress 9.513745e-05 
... Procrustes: rmse 0.1427368  max resid 0.3445499 
Run 37 stress 9.740113e-05 
... Procrustes: rmse 0.07944222  max resid 0.1936961 
Run 38 stress 9.819195e-05 
... Procrustes: rmse 0.0656421  max resid 0.1574147 
Run 39 stress 8.678904e-05 
... Procrustes: rmse 0.107735  max resid 0.261588 
Run 40 stress 8.69852e-05 
... Procrustes: rmse 0.06050472  max resid 0.1448305 
Run 41 stress 9.151744e-05 
... Procrustes: rmse 0.02544703  max resid 0.06006112 
Run 42 stress 9.421919e-05 
... Procrustes: rmse 0.09068855  max resid 0.2165869 
Run 43 stress 0.2249798 
Run 44 stress 9.784529e-05 
... Procrustes: rmse 0.02778264  max resid 0.06596256 
Run 45 stress 9.706405e-05 
... Procrustes: rmse 0.1667612  max resid 0.4081171 
Run 46 stress 9.786297e-05 
... Procrustes: rmse 0.01495359  max resid 0.03512935 
Run 47 stress 7.723104e-05 
... New best solution
... Procrustes: rmse 0.08219489  max resid 0.2004547 
Run 48 stress 9.615278e-05 
... Procrustes: rmse 0.07837847  max resid 0.1855386 
Run 49 stress 9.73395e-05 
... Procrustes: rmse 0.07521555  max resid 0.1624063 
Run 50 stress 7.831879e-05 
... Procrustes: rmse 0.004114803  max resid 0.01001169 
*** No convergence -- monoMDS stopping criteria:
    48: stress < smin
     2: stress ratio > sratmax
stress is (nearly) zero: you may have insufficient data

some squared distances are negative and changed to zero

Run 0 stress 0.004057148 
Run 1 stress 0.0003132056 
... New best solution
... Procrustes: rmse 0.09563141  max resid 0.173432 
Run 2 stress 0.003820962 
Run 3 stress 6.86615e-05 
... New best solution
... Procrustes: rmse 0.0116565  max resid 0.02065372 
Run 4 stress 0.002475264 
Run 5 stress 9.796909e-05 
... Procrustes: rmse 0.0001525007  max resid 0.0003597428 
... Similar to previous best
Run 6 stress 0.0007867326 
Run 7 stress 0.001464736 
Run 8 stress 0.002370016 
Run 9 stress 0.002321086 
Run 10 stress 0.002824514 
Run 11 stress 9.958852e-05 
... Procrustes: rmse 0.002435118  max resid 0.00436641 
... Similar to previous best
Run 12 stress 0.004279178 
Run 13 stress 0.004615126 
Run 14 stress 0.00401314 
Run 15 stress 0.001003602 
Run 16 stress 0.0019895 
Run 17 stress 0.003512334 
Run 18 stress 0.003696047 
Run 19 stress 0.004449227 
Run 20 stress 0.003443399 
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Run 0 stress 9.067646e-05 
Run 1 stress 9.110231e-05 
... Procrustes: rmse 0.0001779459  max resid 0.0002989909 
... Similar to previous best
Run 2 stress 9.627185e-05 
... Procrustes: rmse 0.0001066613  max resid 0.0002234183 
... Similar to previous best
Run 3 stress 9.188034e-05 
... Procrustes: rmse 0.000144028  max resid 0.0002822105 
... Similar to previous best
Run 4 stress 9.42809e-05 
... Procrustes: rmse 0.0001069846  max resid 0.0002163624 
... Similar to previous best
Run 5 stress 9.234793e-05 
... Procrustes: rmse 9.078537e-05  max resid 0.0002245651 
... Similar to previous best
Run 6 stress 9.650997e-05 
... Procrustes: rmse 0.0001000753  max resid 0.0002303269 
... Similar to previous best
Run 7 stress 9.720027e-05 
... Procrustes: rmse 0.0001236748  max resid 0.0002430165 
... Similar to previous best
Run 8 stress 9.961986e-05 
... Procrustes: rmse 5.621712e-05  max resid 9.223319e-05 
... Similar to previous best
Run 9 stress 9.771733e-05 
... Procrustes: rmse 0.0001735538  max resid 0.0003894828 
... Similar to previous best
Run 10 stress 9.169103e-05 
... Procrustes: rmse 8.635932e-05  max resid 0.0001791235 
... Similar to previous best
Run 11 stress 9.675115e-05 
... Procrustes: rmse 9.405712e-05  max resid 0.0002193741 
... Similar to previous best
Run 12 stress 9.699617e-05 
... Procrustes: rmse 0.0002161336  max resid 0.0005675132 
... Similar to previous best
Run 13 stress 9.972287e-05 
... Procrustes: rmse 0.0001013219  max resid 0.0002289973 
... Similar to previous best
Run 14 stress 9.548317e-05 
... Procrustes: rmse 8.897567e-05  max resid 0.0002134352 
... Similar to previous best
Run 15 stress 9.556614e-05 
... Procrustes: rmse 9.665983e-05  max resid 0.0002294433 
... Similar to previous best
Run 16 stress 8.517561e-05 
... New best solution
... Procrustes: rmse 0.0001441305  max resid 0.0002731599 
... Similar to previous best
Run 17 stress 9.660906e-05 
... Procrustes: rmse 0.0001702649  max resid 0.0003421176 
... Similar to previous best
Run 18 stress 9.228205e-05 
... Procrustes: rmse 0.0002270476  max resid 0.0003242311 
... Similar to previous best
Run 19 stress 7.838671e-05 
... New best solution
... Procrustes: rmse 0.0002053979  max resid 0.0004514357 
... Similar to previous best
Run 20 stress 9.675485e-05 
... Procrustes: rmse 0.0002246021  max resid 0.0005204136 
... Similar to previous best
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.06478732 
Run 1 stress 0.06478732 
... New best solution
... Procrustes: rmse 1.991994e-05  max resid 4.444007e-05 
... Similar to previous best
Run 2 stress 0.06478732 
... Procrustes: rmse 4.59711e-06  max resid 6.783002e-06 
... Similar to previous best
Run 3 stress 0.08468917 
Run 4 stress 0.218923 
Run 5 stress 0.2189312 
Run 6 stress 0.3017338 
Run 7 stress 0.08384273 
Run 8 stress 0.301734 
Run 9 stress 0.1238453 
Run 10 stress 0.06478732 
... Procrustes: rmse 1.827482e-05  max resid 4.011759e-05 
... Similar to previous best
Run 11 stress 0.2468083 
Run 12 stress 0.1309035 
Run 13 stress 0.2178622 
Run 14 stress 0.1222038 
Run 15 stress 0.06478732 
... New best solution
... Procrustes: rmse 1.403047e-05  max resid 2.984715e-05 
... Similar to previous best
Run 16 stress 0.08384279 
Run 17 stress 0.06478732 
... New best solution
... Procrustes: rmse 7.778366e-06  max resid 1.613612e-05 
... Similar to previous best
Run 18 stress 0.06478732 
... Procrustes: rmse 1.097479e-05  max resid 2.355169e-05 
... Similar to previous best
Run 19 stress 0.08384276 
Run 20 stress 0.2274463 
*** Solution reached

Run 0 stress 0.0001737962 
Run 1 stress 0.1931245 
Run 2 stress 0.1922478 
Run 3 stress 0.0002433636 
... Procrustes: rmse 0.0006440908  max resid 0.001544935 
... Similar to previous best
Run 4 stress 0.0001469373 
... New best solution
... Procrustes: rmse 0.0006505572  max resid 0.001500907 
... Similar to previous best
Run 5 stress 0.0001690772 
... Procrustes: rmse 0.000678394  max resid 0.001572084 
... Similar to previous best
Run 6 stress 0.0006338134 
... Procrustes: rmse 0.002760331  max resid 0.00385252 
... Similar to previous best
Run 7 stress 9.905228e-05 
... New best solution
... Procrustes: rmse 0.000606058  max resid 0.0009650649 
... Similar to previous best
Run 8 stress 0.0001002189 
... Procrustes: rmse 0.0003396107  max resid 0.0005805789 
... Similar to previous best
Run 9 stress 0.000603401 
Run 10 stress 0.0002985038 
... Procrustes: rmse 0.001452848  max resid 0.00213755 
... Similar to previous best
Run 11 stress 0.192936 
Run 12 stress 0.0002158335 
... Procrustes: rmse 0.0008466959  max resid 0.00127293 
... Similar to previous best
Run 13 stress 0.0002426834 
... Procrustes: rmse 0.0009669963  max resid 0.001426538 
... Similar to previous best
Run 14 stress 0.0001083423 
... Procrustes: rmse 0.0004467831  max resid 0.0007365517 
... Similar to previous best
Run 15 stress 0.0004160257 
... Procrustes: rmse 0.001704275  max resid 0.00244946 
... Similar to previous best
Run 16 stress 9.73418e-05 
... New best solution
... Procrustes: rmse 3.854303e-05  max resid 6.233984e-05 
... Similar to previous best
Run 17 stress 0.0002492047 
... Procrustes: rmse 0.001032235  max resid 0.001547507 
... Similar to previous best
Run 18 stress 9.71039e-05 
... New best solution
... Procrustes: rmse 0.0002951521  max resid 0.0005020085 
... Similar to previous best
Run 19 stress 0.0002124182 
... Procrustes: rmse 0.0007835771  max resid 0.001452022 
... Similar to previous best
Run 20 stress 0.001143199 
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Set of permutations < 'minperm'. Generating entire set.
Set of permutations < 'minperm'. Generating entire set.
Set of permutations < 'minperm'. Generating entire set.
Set of permutations < 'minperm'. Generating entire set.

the matrix is either rank-deficient or indefinite
Run 0 stress 7.005617e-05 
Run 1 stress 0 
... New best solution
... Procrustes: rmse 0.1107594  max resid 0.1620621 
Run 2 stress 0 
... Procrustes: rmse 0.1796376  max resid 0.296941 
Run 3 stress 0 
... Procrustes: rmse 0.1603009  max resid 0.2613614 
Run 4 stress 0 
... Procrustes: rmse 0.1370571  max resid 0.2268672 
Run 5 stress 0.2601588 
Run 6 stress 5.601201e-05 
... Procrustes: rmse 0.1501562  max resid 0.25019 
Run 7 stress 0 
... Procrustes: rmse 0.175267  max resid 0.3406301 
Run 8 stress 7.882424e-05 
... Procrustes: rmse 0.1178408  max resid 0.2233217 
Run 9 stress 0 
... Procrustes: rmse 0.1208735  max resid 0.2365515 
Run 10 stress 0 
... Procrustes: rmse 0.1594542  max resid 0.3395309 
Run 11 stress 0 
... Procrustes: rmse 0.1683528  max resid 0.2825622 
Run 12 stress 0 
... Procrustes: rmse 0.1359023  max resid 0.2316057 
Run 13 stress 0 
... Procrustes: rmse 0.1272357  max resid 0.2125166 
Run 14 stress 0.2913768 
Run 15 stress 0 
... Procrustes: rmse 0.1594966  max resid 0.348734 
Run 16 stress 0 
... Procrustes: rmse 0.1480589  max resid 0.3209884 
Run 17 stress 0 
... Procrustes: rmse 0.1396237  max resid 0.2583611 
Run 18 stress 0 
... Procrustes: rmse 0.1802635  max resid 0.3671116 
Run 19 stress 0 
... Procrustes: rmse 0.1088744  max resid 0.1581856 
Run 20 stress 0 
... Procrustes: rmse 0.140263  max resid 0.1975136 
Run 21 stress 0 
... Procrustes: rmse 0.1679227  max resid 0.2902029 
Run 22 stress 0 
... Procrustes: rmse 0.1080097  max resid 0.1884412 
Run 23 stress 4.096519e-05 
... Procrustes: rmse 0.1460704  max resid 0.3262926 
Run 24 stress 0 
... Procrustes: rmse 0.1768473  max resid 0.3074839 
Run 25 stress 0.260151 
Run 26 stress 0 
... Procrustes: rmse 0.1433172  max resid 0.2840299 
Run 27 stress 0 
... Procrustes: rmse 0.1310975  max resid 0.2911339 
Run 28 stress 0 
... Procrustes: rmse 0.1909139  max resid 0.3431758 
Run 29 stress 0 
... Procrustes: rmse 0.1359499  max resid 0.2487249 
Run 30 stress 0.260161 
Run 31 stress 0 
... Procrustes: rmse 0.1477025  max resid 0.2357143 
Run 32 stress 0 
... Procrustes: rmse 0.1334867  max resid 0.2737578 
Run 33 stress 0 
... Procrustes: rmse 0.186326  max resid 0.2922697 
Run 34 stress 0 
... Procrustes: rmse 0.1267352  max resid 0.2841199 
Run 35 stress 8.700007e-05 
... Procrustes: rmse 0.1811012  max resid 0.3637296 
Run 36 stress 0 
... Procrustes: rmse 0.1555964  max resid 0.331628 
Run 37 stress 0 
... Procrustes: rmse 0.1448856  max resid 0.231232 
Run 38 stress 4.74369e-05 
... Procrustes: rmse 0.1453227  max resid 0.2714403 
Run 39 stress 0 
... Procrustes: rmse 0.1162664  max resid 0.2549876 
Run 40 stress 0 
... Procrustes: rmse 0.07351639  max resid 0.09561597 
Run 41 stress 0 
... Procrustes: rmse 0.1520385  max resid 0.2624539 
Run 42 stress 0 
... Procrustes: rmse 0.1503577  max resid 0.2311533 
Run 43 stress 8.33597e-05 
... Procrustes: rmse 0.1054097  max resid 0.1683178 
Run 44 stress 0 
... Procrustes: rmse 0.05465973  max resid 0.07291582 
Run 45 stress 3.410929e-05 
... Procrustes: rmse 0.1521829  max resid 0.2687246 
Run 46 stress 0 
... Procrustes: rmse 0.1337994  max resid 0.2301535 
Run 47 stress 0 
... Procrustes: rmse 0.123918  max resid 0.2469821 
Run 48 stress 5.73814e-05 
... Procrustes: rmse 0.1243357  max resid 0.2026426 
Run 49 stress 0 
... Procrustes: rmse 0.1422029  max resid 0.2488459 
Run 50 stress 0 
... Procrustes: rmse 0.155961  max resid 0.3128638 
*** No convergence -- monoMDS stopping criteria:
    46: stress < smin
     4: stress ratio > sratmax
stress is (nearly) zero: you may have insufficient data

some squared distances are negative and changed to zero

Run 0 stress 8.721965e-05 
Run 1 stress 9.495963e-05 
... Procrustes: rmse 0.0752607  max resid 0.1856571 
Run 2 stress 9.709662e-05 
... Procrustes: rmse 0.1298015  max resid 0.2482023 
Run 3 stress 0.0002908939 
... Procrustes: rmse 0.1163453  max resid 0.261744 
Run 4 stress 9.737233e-05 
... Procrustes: rmse 0.1839662  max resid 0.4454657 
Run 5 stress 9.915997e-05 
... Procrustes: rmse 0.1683944  max resid 0.4424191 
Run 6 stress 8.933734e-05 
... Procrustes: rmse 0.1717334  max resid 0.4424444 
Run 7 stress 9.063125e-05 
... Procrustes: rmse 0.1290613  max resid 0.2966678 
Run 8 stress 9.652917e-05 
... Procrustes: rmse 0.122026  max resid 0.2911875 
Run 9 stress 8.721457e-05 
... New best solution
... Procrustes: rmse 0.09269199  max resid 0.2044008 
Run 10 stress 0.0002030336 
... Procrustes: rmse 0.1650057  max resid 0.4308755 
Run 11 stress 8.954966e-05 
... Procrustes: rmse 0.1891889  max resid 0.4601668 
Run 12 stress 0.0004168325 
... Procrustes: rmse 0.1882785  max resid 0.4711072 
Run 13 stress 9.899608e-05 
... Procrustes: rmse 0.1746658  max resid 0.4501998 
Run 14 stress 9.779146e-05 
... Procrustes: rmse 0.1945713  max resid 0.4570796 
Run 15 stress 2.295362e-07 
... New best solution
... Procrustes: rmse 0.2096509  max resid 0.5417649 
Run 16 stress 8.43171e-05 
... Procrustes: rmse 0.1464804  max resid 0.3160826 
Run 17 stress 8.269528e-05 
... Procrustes: rmse 0.08111843  max resid 0.1694908 
Run 18 stress 9.611796e-05 
... Procrustes: rmse 0.06059572  max resid 0.1441053 
Run 19 stress 0.000583308 
Run 20 stress 7.926188e-05 
... Procrustes: rmse 0.09739839  max resid 0.2342326 
Run 21 stress 7.08114e-05 
... Procrustes: rmse 0.05497349  max resid 0.1434307 
Run 22 stress 9.60515e-05 
... Procrustes: rmse 0.2081029  max resid 0.3967444 
Run 23 stress 9.985001e-05 
... Procrustes: rmse 0.1822  max resid 0.3268183 
Run 24 stress 9.523672e-05 
... Procrustes: rmse 0.1277837  max resid 0.2870385 
Run 25 stress 9.880334e-05 
... Procrustes: rmse 0.1691981  max resid 0.3453624 
Run 26 stress 9.797208e-05 
... Procrustes: rmse 0.1943246  max resid 0.3932757 
Run 27 stress 7.991742e-05 
... Procrustes: rmse 0.1897103  max resid 0.3489437 
Run 28 stress 9.827434e-05 
... Procrustes: rmse 0.1601055  max resid 0.3465772 
Run 29 stress 9.902841e-05 
... Procrustes: rmse 0.1579787  max resid 0.315932 
Run 30 stress 9.411416e-05 
... Procrustes: rmse 0.1804202  max resid 0.3870789 
Run 31 stress 9.302819e-05 
... Procrustes: rmse 0.08922465  max resid 0.1891959 
Run 32 stress 8.65736e-05 
... Procrustes: rmse 0.1894873  max resid 0.3524702 
Run 33 stress 9.718201e-05 
... Procrustes: rmse 0.1549785  max resid 0.3107519 
Run 34 stress 5.462037e-05 
... Procrustes: rmse 0.04579491  max resid 0.1272207 
Run 35 stress 9.204787e-05 
... Procrustes: rmse 0.164304  max resid 0.3518353 
Run 36 stress 9.954443e-05 
... Procrustes: rmse 0.1778288  max resid 0.4212087 
Run 37 stress 9.533226e-05 
... Procrustes: rmse 0.1582482  max resid 0.3399884 
Run 38 stress 0.0003033731 
... Procrustes: rmse 0.1296228  max resid 0.2192902 
Run 39 stress 9.385977e-05 
... Procrustes: rmse 0.1774193  max resid 0.3570189 
Run 40 stress 0.0003136235 
... Procrustes: rmse 0.105874  max resid 0.220973 
Run 41 stress 7.00375e-05 
... Procrustes: rmse 0.08064397  max resid 0.2193751 
Run 42 stress 9.224654e-10 
... New best solution
... Procrustes: rmse 0.02366539  max resid 0.06630255 
Run 43 stress 0.0001876882 
... Procrustes: rmse 0.1343535  max resid 0.3226501 
Run 44 stress 8.217977e-05 
... Procrustes: rmse 0.01139482  max resid 0.03152576 
Run 45 stress 0.0006526166 
Run 46 stress 9.822717e-05 
... Procrustes: rmse 0.1698526  max resid 0.3530765 
Run 47 stress 9.487946e-05 
... Procrustes: rmse 0.09787196  max resid 0.2184816 
Run 48 stress 9.952979e-05 
... Procrustes: rmse 0.1930848  max resid 0.3729796 
Run 49 stress 9.782336e-05 
... Procrustes: rmse 0.1757682  max resid 0.3737311 
Run 50 stress 0.0005531539 
*** No convergence -- monoMDS stopping criteria:
     9: no. of iterations >= maxit
    41: stress < smin
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.001330486 
Run 1 stress 0.0102618 
Run 2 stress 0.01068341 
Run 3 stress 0.0101777 
Run 4 stress 0.01011898 
Run 5 stress 0.01074989 
Run 6 stress 0.009865147 
Run 7 stress 0.001455574 
... Procrustes: rmse 0.002008137  max resid 0.003504469 
... Similar to previous best
Run 8 stress 0.01026857 
Run 9 stress 0.002942602 
Run 10 stress 0.001258874 
... New best solution
... Procrustes: rmse 0.001137115  max resid 0.001987802 
... Similar to previous best
Run 11 stress 0.01036499 
Run 12 stress 0.01006273 
Run 13 stress 0.001096652 
... New best solution
... Procrustes: rmse 0.002649618  max resid 0.004636221 
... Similar to previous best
Run 14 stress 0.01033084 
Run 15 stress 0.01038906 
Run 16 stress 0.0006190737 
... New best solution
... Procrustes: rmse 0.02161587  max resid 0.03826 
Run 17 stress 0.003199082 
Run 18 stress 0.002976297 
Run 19 stress 0.002914593 
Run 20 stress 0.1776138 
Run 21 stress 0.01054381 
Run 22 stress 0.0011561 
Run 23 stress 0.009984864 
Run 24 stress 0.1776123 
Run 25 stress 0.0008842209 
... Procrustes: rmse 0.002038128  max resid 0.003713254 
... Similar to previous best
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.003910892 
Run 1 stress 0.01767479 
Run 2 stress 0.006896669 
Run 3 stress 0.004224086 
... Procrustes: rmse 0.008537337  max resid 0.02009377 
Run 4 stress 0.01742178 
Run 5 stress 0.00784041 
Run 6 stress 0.006803662 
Run 7 stress 0.01746948 
Run 8 stress 0.2380299 
Run 9 stress 0.0174127 
Run 10 stress 0.1579801 
Run 11 stress 0.00489736 
Run 12 stress 0.1946672 
Run 13 stress 0.0180764 
Run 14 stress 0.004218569 
... Procrustes: rmse 0.008802041  max resid 0.0206495 
Run 15 stress 0.004998118 
Run 16 stress 0.2005064 
Run 17 stress 0.004134582 
... Procrustes: rmse 0.007469317  max resid 0.01764092 
Run 18 stress 0.01741947 
Run 19 stress 0.004016489 
... Procrustes: rmse 0.005170946  max resid 0.01217771 
Run 20 stress 0.006803634 
Run 21 stress 0.01745716 
Run 22 stress 0.004073168 
... Procrustes: rmse 0.006764288  max resid 0.01597491 
Run 23 stress 0.01814757 
Run 24 stress 0.1579716 
Run 25 stress 0.003981175 
... Procrustes: rmse 0.003910477  max resid 0.009209736 
... Similar to previous best
*** Solution reached

Run 0 stress 0.1006496 
Run 1 stress 0.1031526 
Run 2 stress 0.1031526 
Run 3 stress 0.1951269 
Run 4 stress 0.1597999 
Run 5 stress 0.1640799 
Run 6 stress 0.1083668 
Run 7 stress 0.1083617 
Run 8 stress 0.1641053 
Run 9 stress 0.3100932 
Run 10 stress 0.1035243 
Run 11 stress 0.2103553 
Run 12 stress 0.1031522 
Run 13 stress 0.1083657 
Run 14 stress 0.1951269 
Run 15 stress 0.2374606 
Run 16 stress 0.1035243 
Run 17 stress 0.2098428 
Run 18 stress 0.1629503 
Run 19 stress 0.1035244 
Run 20 stress 0.1035245 
Run 21 stress 0.1035246 
Run 22 stress 0.2268951 
Run 23 stress 0.1951269 
Run 24 stress 0.1598002 
Run 25 stress 0.1035245 
Run 26 stress 0.1031521 
Run 27 stress 0.1640513 
Run 28 stress 0.1630402 
Run 29 stress 0.1640898 
Run 30 stress 0.161274 
Run 31 stress 0.1035243 
Run 32 stress 0.103152 
Run 33 stress 0.1630402 
Run 34 stress 0.1031522 
Run 35 stress 0.1006497 
... Procrustes: rmse 0.0001298946  max resid 0.0002462838 
... Similar to previous best
*** Solution reached

Run 0 stress 0.003726447 
Run 1 stress 0.0009149695 
... New best solution
... Procrustes: rmse 0.02844682  max resid 0.04292799 
Run 2 stress 0.3209238 
Run 3 stress 0.001159242 
... Procrustes: rmse 0.001153499  max resid 0.00166699 
... Similar to previous best
Run 4 stress 0.0002495404 
... New best solution
... Procrustes: rmse 0.003605675  max resid 0.005143764 
... Similar to previous best
Run 5 stress 0.0001886906 
... New best solution
... Procrustes: rmse 0.0002580389  max resid 0.000353918 
... Similar to previous best
Run 6 stress 0.002553226 
Run 7 stress 0.0004351715 
... Procrustes: rmse 0.001598463  max resid 0.00248278 
... Similar to previous best
Run 8 stress 0.0009720799 
Run 9 stress 0.008038564 
Run 10 stress 0.001897718 
Run 11 stress 0.008382712 
Run 12 stress 0.005082917 
Run 13 stress 0.001027933 
Run 14 stress 0.003232986 
Run 15 stress 0.006398985 
Run 16 stress 0.0037748 
Run 17 stress 0.005736606 
Run 18 stress 9.904321e-05 
... New best solution
... Procrustes: rmse 0.0005232668  max resid 0.0009571667 
... Similar to previous best
Run 19 stress 0.3209238 
Run 20 stress 0.0009093694 
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.009886766 
Run 1 stress 0.009886895 
... Procrustes: rmse 4.4742e-05  max resid 6.820768e-05 
... Similar to previous best
Run 2 stress 0.009886792 
... Procrustes: rmse 2.660776e-05  max resid 4.872767e-05 
... Similar to previous best
Run 3 stress 0.009887335 
... Procrustes: rmse 0.0007348911  max resid 0.001012578 
... Similar to previous best
Run 4 stress 0.01181363 
Run 5 stress 0.01181326 
Run 6 stress 0.01181387 
Run 7 stress 0.009887669 
... Procrustes: rmse 0.0002639188  max resid 0.0003577166 
... Similar to previous best
Run 8 stress 0.003137305 
... New best solution
... Procrustes: rmse 0.1486293  max resid 0.2778697 
Run 9 stress 0.01181365 
Run 10 stress 0.01181345 
Run 11 stress 0.01181296 
Run 12 stress 0.009887095 
Run 13 stress 0.01181365 
Run 14 stress 0.0118136 
Run 15 stress 0.009887865 
Run 16 stress 0.001644788 
... New best solution
... Procrustes: rmse 0.00570225  max resid 0.007827323 
Run 17 stress 0.009887305 
Run 18 stress 0.009887326 
Run 19 stress 0.009895394 
Run 20 stress 0.01181307 
Run 21 stress 0.3209238 
Run 22 stress 0.01181312 
Run 23 stress 0.00988735 
Run 24 stress 0.01181334 
Run 25 stress 0.002179876 
Run 26 stress 0.01181389 
Run 27 stress 0.009886813 
Run 28 stress 0.01181368 
Run 29 stress 0.01181331 
Run 30 stress 0.01181327 
Run 31 stress 0.2958243 
Run 32 stress 0.0118134 
Run 33 stress 0.01181344 
Run 34 stress 0.01181327 
Run 35 stress 0.009887246 
Run 36 stress 0.01181372 
Run 37 stress 0.01181351 
Run 38 stress 0.01181346 
Run 39 stress 0.01181296 
Run 40 stress 0.009887811 
Run 41 stress 0.2834628 
Run 42 stress 0.01181342 
Run 43 stress 0.01181365 
Run 44 stress 0.01181335 
Run 45 stress 0.009888144 
Run 46 stress 0.009887007 
Run 47 stress 0.01181356 
Run 48 stress 0.009887006 
Run 49 stress 0.01181306 
Run 50 stress 0.01181297 
*** No convergence -- monoMDS stopping criteria:
     5: no. of iterations >= maxit
    45: stress ratio > sratmax

Run 0 stress 0.0008020932 
Run 1 stress 9.750691e-05 
... New best solution
... Procrustes: rmse 0.005116532  max resid 0.01010663 
Run 2 stress 8.201927e-05 
... New best solution
... Procrustes: rmse 4.230489e-05  max resid 8.577289e-05 
... Similar to previous best
Run 3 stress 0.003095419 
Run 4 stress 9.747516e-05 
... Procrustes: rmse 0.0001994593  max resid 0.0003831759 
... Similar to previous best
Run 5 stress 9.62684e-05 
... Procrustes: rmse 0.0001480487  max resid 0.0002623351 
... Similar to previous best
Run 6 stress 0.001049042 
Run 7 stress 9.805017e-05 
... Procrustes: rmse 0.0002148108  max resid 0.0003794942 
... Similar to previous best
Run 8 stress 9.988109e-05 
... Procrustes: rmse 0.0004962097  max resid 0.0007997795 
... Similar to previous best
Run 9 stress 9.654156e-05 
... Procrustes: rmse 3.960846e-05  max resid 8.15097e-05 
... Similar to previous best
Run 10 stress 0.001782582 
Run 11 stress 0.0004128235 
... Procrustes: rmse 0.002564904  max resid 0.005030343 
... Similar to previous best
Run 12 stress 0.001249741 
Run 13 stress 0.001739429 
Run 14 stress 0.00223367 
Run 15 stress 0.0003976754 
... Procrustes: rmse 0.002468066  max resid 0.004829322 
... Similar to previous best
Run 16 stress 8.279852e-05 
... Procrustes: rmse 0.000216879  max resid 0.0003501307 
... Similar to previous best
Run 17 stress 0.001141836 
Run 18 stress 9.424054e-05 
... Procrustes: rmse 0.0001940248  max resid 0.0003631561 
... Similar to previous best
Run 19 stress 0.001593474 
Run 20 stress 0.0005702038 
... Procrustes: rmse 0.003608715  max resid 0.007123898 
... Similar to previous best
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.02472531 
Run 1 stress 0.02617798 
Run 2 stress 0.05285309 
Run 3 stress 0.05285051 
Run 4 stress 0.03732498 
Run 5 stress 0.04150701 
Run 6 stress 0.02472567 
... Procrustes: rmse 0.000229733  max resid 0.0004080513 
... Similar to previous best
Run 7 stress 0.05285139 
Run 8 stress 0.02617855 
Run 9 stress 0.05285179 
Run 10 stress 0.04022859 
Run 11 stress 0.04150743 
Run 12 stress 0.301653 
Run 13 stress 0.05285061 
Run 14 stress 0.02617792 
Run 15 stress 0.03732486 
Run 16 stress 0.02617779 
Run 17 stress 0.03732444 
Run 18 stress 0.04022848 
Run 19 stress 0.02472566 
... Procrustes: rmse 0.0005635939  max resid 0.00102827 
... Similar to previous best
Run 20 stress 0.02617833 
*** Solution reached

Run 0 stress 0.004654572 
Run 1 stress 0.004561244 
... New best solution
... Procrustes: rmse 0.002390258  max resid 0.005049396 
... Similar to previous best
Run 2 stress 0.005741514 
Run 3 stress 0.0008310096 
... New best solution
... Procrustes: rmse 0.1096484  max resid 0.2378611 
Run 4 stress 9.855991e-05 
... New best solution
... Procrustes: rmse 0.03548357  max resid 0.07626931 
Run 5 stress 9.905774e-05 
... Procrustes: rmse 0.0002814818  max resid 0.0005079338 
... Similar to previous best
Run 6 stress 0.0001503091 
... Procrustes: rmse 0.006685041  max resid 0.01460539 
Run 7 stress 0.001230588 
Run 8 stress 0.3208797 
Run 9 stress 9.694505e-05 
... New best solution
... Procrustes: rmse 0.0002783379  max resid 0.0004954861 
... Similar to previous best
Run 10 stress 0.002387915 
Run 11 stress 9.590866e-05 
... New best solution
... Procrustes: rmse 2.062539e-05  max resid 3.436255e-05 
... Similar to previous best
Run 12 stress 0.002054987 
Run 13 stress 9.733518e-05 
... Procrustes: rmse 0.0002204859  max resid 0.0004065847 
... Similar to previous best
Run 14 stress 0.002523767 
Run 15 stress 0.003432957 
Run 16 stress 0.004301808 
Run 17 stress 0.001559285 
Run 18 stress 0.002766787 
Run 19 stress 0.001771348 
Run 20 stress 9.859705e-05 
... Procrustes: rmse 2.374201e-05  max resid 4.710894e-05 
... Similar to previous best
*** Solution reached
stress is (nearly) zero: you may have insufficient data

Run 0 stress 0.01498623 
Run 1 stress 0.01498611 
... New best solution
... Procrustes: rmse 0.0001193423  max resid 0.0002216734 
... Similar to previous best
Run 2 stress 0.01498609 
... New best solution
... Procrustes: rmse 1.773182e-05  max resid 2.390395e-05 
... Similar to previous best
Run 3 stress 0.3209238 
Run 4 stress 0.01498617 
... Procrustes: rmse 8.827194e-05  max resid 0.0001580609 
... Similar to previous best
Run 5 stress 0.2583166 
Run 6 stress 0.01498609 
... Procrustes: rmse 2.014819e-05  max resid 3.335632e-05 
... Similar to previous best
Run 7 stress 0.301736 
Run 8 stress 0.01498651 
... Procrustes: rmse 0.0001554673  max resid 0.0002823505 
... Similar to previous best
Run 9 stress 0.01498619 
... Procrustes: rmse 0.0001052337  max resid 0.0001877758 
... Similar to previous best
Run 10 stress 0.1433568 
Run 11 stress 0.0149864 
... Procrustes: rmse 0.0001855524  max resid 0.0003442151 
... Similar to previous best
Run 12 stress 0.01498637 
... Procrustes: rmse 0.0001795198  max resid 0.000332003 
... Similar to previous best
Run 13 stress 0.01498626 
... Procrustes: rmse 0.0001342418  max resid 0.0002461645 
... Similar to previous best
Run 14 stress 0.1287859 
Run 15 stress 0.01498609 
... Procrustes: rmse 4.749228e-06  max resid 6.683217e-06 
... Similar to previous best
Run 16 stress 0.01498634 
... Procrustes: rmse 0.0001563341  max resid 0.0002864291 
... Similar to previous best
Run 17 stress 0.01498622 
... Procrustes: rmse 0.0001114253  max resid 0.0002008367 
... Similar to previous best
Run 18 stress 0.01498611 
... Procrustes: rmse 3.89444e-05  max resid 6.233891e-05 
... Similar to previous best
Run 19 stress 0.01498615 
... Procrustes: rmse 7.650915e-05  max resid 0.0001353694 
... Similar to previous best
Run 20 stress 0.1287859 
*** Solution reached

[[1]]
[[1]][[1]]
$sites
                PCoA1         PCoA2
VRP_1_2  0.5862686842  5.000000e-01
VRP_3_2 -0.1047214513 -1.570092e-15
VRP_1_3 -0.2763765091  1.030373e-15
VRP_2_1 -0.2642310057  1.167756e-15
VRP_2_2  0.0254217337 -4.035628e-15
VRP_2_3 -0.2757490867  1.246261e-15
VRP_3_1 -0.2763765091  1.246261e-15
VRP_3_3 -0.0005045401 -3.576867e-15
VRP_1_1  0.5862686842 -5.000000e-01

$centroids
       PCoA1         PCoA2
1  0.2987202  3.338430e-15
2 -0.2449256  7.621935e-16
3 -0.1392895 -1.083007e-15

attr(,"class")
[1] "ordiplot"

[[1]][[2]]
[[1]][[2]]$x
 [1] 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000
 [9] 0.60000000 0.60000000 0.73076923 0.60000000 0.60000000 0.70879121 1.00000000 0.21250000
[17] 0.73076923 0.06722689 0.00000000 0.70879121 1.00000000 0.73076923 0.21250000 0.21250000
[25] 0.70879121 1.00000000 0.73076923 0.73076923 0.73076923 1.00000000 0.06722689 0.70879121
[33] 1.00000000 0.70879121 1.00000000 1.00000000

[[1]][[2]]$y
 [1] 4.238532e+00 4.439044e+00 4.443675e+00 3.204349e+00 4.439497e+00 4.439044e+00
 [7] 3.830185e+00 4.570788e+00 2.359216e-01 2.413218e-01 1.323542e+00 2.364503e-01
[13] 2.359216e-01 4.959681e-01 4.238532e+00 5.400175e-03 1.559464e+00 5.286974e-04
[19] 2.773856e-16 7.318897e-01 4.439044e+00 1.564864e+00 4.871477e-03 5.400175e-03
[25] 7.372899e-01 4.443675e+00 1.559993e+00 1.559464e+00 8.275744e-01 3.204349e+00
[31] 5.286974e-04 7.324184e-01 4.439497e+00 7.318897e-01 4.439044e+00 3.830185e+00

[[1]][[2]]$yf
 [1] 4.238532e+00 4.439044e+00 4.443675e+00 3.204349e+00 4.439497e+00 4.439044e+00
 [7] 3.830185e+00 4.570788e+00 2.359216e-01 2.413218e-01 1.323542e+00 2.364503e-01
[13] 2.359216e-01 4.959681e-01 4.238532e+00 5.400175e-03 1.559464e+00 5.286974e-04
[19] 2.773856e-16 7.318897e-01 4.439044e+00 1.564864e+00 4.871477e-03 5.400175e-03
[25] 7.372899e-01 4.443675e+00 1.559993e+00 1.559464e+00 8.275744e-01 3.204349e+00
[31] 5.286974e-04 7.324184e-01 4.439497e+00 7.318897e-01 4.439044e+00 3.830185e+00


[[1]][[3]]


[[2]]
[[2]][[1]]
$sites
              PCoA1       PCoA2
VRP_2_2  0.06223194 -0.03218835
VRP_3_2 -0.12143039 -0.08428135
VRP_1_1 -0.03924415  0.41973318
VRP_1_2 -0.30722804 -0.03446703
VRP_1_3  0.09108614 -0.18428576
VRP_2_1  0.18101590  0.01197154
VRP_2_3  0.25283684  0.01347461
VRP_3_3  0.06108066 -0.04542514
VRP_3_1 -0.18034891 -0.06453169

$centroids
        PCoA1        PCoA2
1 -0.11745679  0.034163892
2  0.18962177  0.004250358
3 -0.09201998 -0.065915552

attr(,"class")
[1] "ordiplot"

[[2]][[2]]
[[2]][[2]]$x
 [1] 0.5032051 0.6149790 0.5334101 0.5153319 0.5238848 0.5045845 0.4845350 0.5407875 0.5551639
[10] 0.3723634 0.3907011 0.4637906 0.4803642 0.3952268 0.3411745 0.5531478 0.6345116 0.5139555
[19] 0.5580446 0.5428889 0.5501391 0.4873470 0.5354037 0.5966125 0.4939780 0.2518451 0.3496873
[28] 0.4210040 0.3861088 0.4290666 0.3222381 0.3551889 0.4182878 0.4359211 0.4909468 0.3807462

[[2]][[2]]$y
 [1] 0.4600318 1.1179237 0.6920834 0.3168000 0.6058212 0.4570879 0.4929546 0.6270031 0.8068699
[10] 0.2514792 0.2203721 0.4396437 0.5146830 0.2496545 0.2067686 0.8310892 0.8118237 0.5255981
[19] 0.7589168 0.6332716 0.6100067 0.4701074 0.6152138 0.7468399 0.4461997 0.2694334 0.3299042
[28] 0.3118611 0.1792103 0.3245754 0.2500015 0.1904821 0.3530236 0.3123646 0.5246327 0.2126948

[[2]][[2]]$yf
 [1] 0.4675661 0.9648737 0.6355157 0.4675661 0.6058212 0.4675661 0.4675661 0.6355157 0.7859290
[10] 0.2344829 0.2344829 0.4396437 0.4675661 0.2496545 0.2344829 0.7859290 0.9648737 0.4675661
[19] 0.7859290 0.6355157 0.6355157 0.4675661 0.6355157 0.7859290 0.4675661 0.2344829 0.2344829
[28] 0.3254562 0.2344829 0.3254562 0.2344829 0.2344829 0.3254562 0.3254562 0.4675661 0.2344829


[[2]][[3]]


[[3]]
[[3]][[1]]
$sites
               PCoA1         PCoA2
VRP_3_1  0.029052046 -0.0047338085
VRP_1_1 -0.055733432  0.0205083265
VRP_1_2 -0.027371046 -0.0315120710
VRP_1_3  0.005723366  0.0009047258
VRP_2_1  0.008891801 -0.0052788598
VRP_2_2  0.003247065  0.0057336522
VRP_2_3  0.016370296  0.0472680986
VRP_3_2  0.011433932 -0.0186441995
VRP_3_3  0.008385972 -0.0142458642

$centroids
         PCoA1        PCoA2
1 -0.024920004 -0.006837472
2  0.006780712  0.008980220
3  0.013529282 -0.013588374

attr(,"class")
[1] "ordiplot"

[[3]][[2]]
[[3]][[2]]$x
 [1] 0.09118262 0.06679724 0.04947584 0.05116147 0.04731814 0.05931034 0.04486558 0.03817052
 [9] 0.06459339 0.07212132 0.07754841 0.06646357 0.07921552 0.08064126 0.07488133 0.06023513
[17] 0.05759675 0.05838419 0.09088092 0.05358339 0.05174796 0.04378628 0.04179200 0.05981422
[25] 0.04285236 0.04162236 0.03329178 0.06307684 0.04244733 0.04202763 0.05350693 0.04113854
[33] 0.03983053 0.07057321 0.06692789 0.02945824

[[3]][[2]]$y
 [1] 0.0912955449 0.0681278354 0.0106406370 0.0160599952 0.0179234013 0.0623067436
 [7] 0.0137044791 0.0129804829 0.0579051267 0.0806564366 0.0759031964 0.0735214797
[13] 0.0780084706 0.0826461566 0.0826011211 0.0601541573 0.0538897075 0.0539181511
[19] 0.0975457191 0.0545952429 0.0552217927 0.0063052412 0.0074122219 0.0574332770
[25] 0.0100198644 0.0090984181 0.0031148412 0.0594722408 0.0085996225 0.0080320632
[31] 0.0567901432 0.0117141342 0.0111408031 0.0671349079 0.0662823246 0.0009434977

[[3]][[2]]$yf
 [1] 0.0944206320 0.0687666369 0.0142820192 0.0160599952 0.0142820192 0.0594543091
 [7] 0.0137044791 0.0094780946 0.0594543091 0.0792923062 0.0792923062 0.0687666369
[13] 0.0792923062 0.0826461566 0.0792923062 0.0594543091 0.0548830075 0.0548830075
[19] 0.0944206320 0.0548830075 0.0548830075 0.0094780946 0.0094780946 0.0594543091
[25] 0.0094780946 0.0094780946 0.0031148412 0.0594543091 0.0094780946 0.0094780946
[31] 0.0548830075 0.0094780946 0.0094780946 0.0687666369 0.0687666369 0.0009434977


[[3]][[3]]


[[4]]
[[4]][[1]]
$sites
             PCoA1        PCoA2
VRP_2_3  0.3449351  0.115830925
VRP_3_1  0.3522500 -0.224617031
VRP_2_2 -0.1740941 -0.018454748
VRP_1_1 -0.1582541 -0.020485535
VRP_1_2 -0.1780778  0.012370314
VRP_1_3  0.3828341  0.105291041
VRP_2_1 -0.1784519  0.027414389
VRP_3_2 -0.1967549 -0.005775657
VRP_3_3 -0.1943863  0.008426301

$centroids
       PCoA1        PCoA2
1 -0.1398127 -0.004960608
2 -0.1461517  0.015793066
3 -0.1863440 -0.003347964

attr(,"class")
[1] "ordiplot"

[[4]][[2]]
[[4]][[2]]$x
 [1] 0.34351650 0.55883229 0.54612438 0.53434534 0.17224712 0.53252109 0.55498082 0.54919820
 [9] 0.56712642 0.55352480 0.58222433 0.34965670 0.59102600 0.59323452 0.59564535 0.05415415
[17] 0.07258085 0.56305667 0.06008295 0.08218148 0.07318827 0.07803641 0.54948760 0.08227694
[25] 0.10994541 0.09560619 0.58225731 0.10210716 0.06351451 0.05162704 0.58513639 0.60672609
[33] 0.60048775 0.12069414 0.11217268 0.03539800

[[4]][[2]]$y
 [1] 0.5859078343 1.0367568538 1.0366357009 1.0367336909 0.4858224942 1.0367496365
 [7] 1.0369402657 1.0368135824 1.0369230413 1.0367997780 1.0367984550 1.0357483844
[13] 1.0370382712 1.0369392367 1.0368247813 0.0001274544 0.0001953007 1.0370496793
[19] 0.0002238863 0.0003136825 0.0002751228 0.0001828117 1.0369598551 0.0002869282
[25] 0.0003727344 0.0002904552 1.0371173882 0.0004179934 0.0002152607 0.0001097713
[31] 1.0369413256 1.0373288631 1.0372227994 0.0005148538 0.0004971158 0.0001275395

[[4]][[2]]$yf
 [1] 0.5859078343 1.0368641881 1.0367063428 1.0367063428 0.4858224942 1.0367063428
 [7] 1.0368641881 1.0368135824 1.0369237252 1.0368641881 1.0369237252 1.0357483844
[13] 1.0369722006 1.0369722006 1.0369722006 0.0001274544 0.0002114826 1.0369237252
[19] 0.0002114826 0.0002970219 0.0002289672 0.0002289672 1.0368641881 0.0002970219
[25] 0.0003953639 0.0002970219 1.0369722006 0.0003953639 0.0002114826 0.0001186554
[31] 1.0369722006 1.0373288631 1.0372227994 0.0005148538 0.0004971158 0.0001186554


[[4]][[3]]


[[5]]
[[5]][[1]]
$sites
               PCoA1        PCoA2
VRP_3_1 -0.078753712 -0.011303242
VRP_1_2 -0.158482581  0.159849075
VRP_3_2 -0.054120998  0.005917372
VRP_1_3 -0.095069288 -0.056606724
VRP_2_1 -0.003542966 -0.117214228
VRP_2_2 -0.088084421 -0.012443024
VRP_2_3  0.056884088 -0.070588143
VRP_3_3 -0.134244891  0.050724267
VRP_1_1  0.555414768  0.051664647

$centroids
        PCoA1        PCoA2
1 -0.05641014  0.015386273
2 -0.00498768 -0.097158767
3 -0.06603741  0.008252513

attr(,"class")
[1] "ordiplot"

[[5]][[2]]
[[5]][[2]]$x
 [1] 0.19953601 0.08615449 0.06644644 0.13742331 0.03890593 0.21793879 0.15793554 0.63870983
 [9] 0.19600840 0.24012520 0.31184462 0.21583370 0.33374020 0.14258375 0.72366111 0.10472028
[17] 0.14772727 0.11722488 0.15247588 0.10656912 0.61350068 0.12316093 0.05752362 0.20974035
[25] 0.13696550 0.65936008 0.16297588 0.11404617 0.24599799 0.58575638 0.24837058 0.16429344
[33] 0.64974470 0.21232877 0.52599433 0.69525659

[[5]][[2]]$y
 [1] 2.029188e-04 8.472393e-05 2.604755e-05 2.499066e-04 2.882273e-05 2.906740e-04
 [7] 1.638216e-04 1.128394e+00 2.411203e-04 2.080866e-04 2.590841e-04 2.119123e-04
[13] 3.069065e-04 3.213432e-04 1.128586e+00 5.910499e-05 1.899850e-04 5.593277e-05
[19] 2.233910e-04 8.522818e-05 1.128345e+00 2.274649e-04 4.164064e-06 2.669564e-04
[25] 1.404602e-04 1.128382e+00 2.270434e-04 4.858523e-05 2.003562e-04 1.128405e+00
[31] 2.660566e-04 1.366376e-04 1.128378e+00 2.167423e-04 1.128378e+00 1.128267e+00

[[5]][[2]]$yf
 [1] 2.220196e-04 6.671502e-05 2.604755e-05 2.160183e-04 1.649340e-05 2.330389e-04
 [7] 2.160183e-04 1.128364e+00 2.220196e-04 2.330389e-04 2.625704e-04 2.318703e-04
[13] 3.069065e-04 2.160183e-04 1.128586e+00 6.671502e-05 2.160183e-04 6.671502e-05
[19] 2.160183e-04 6.671502e-05 1.128364e+00 1.839625e-04 1.649340e-05 2.318703e-04
[25] 1.839625e-04 1.128364e+00 2.160183e-04 6.671502e-05 2.330389e-04 1.128364e+00
[31] 2.625704e-04 2.160183e-04 1.128364e+00 2.318703e-04 1.128364e+00 1.128364e+00


[[5]][[3]]


[[6]]
[[6]][[1]]
$sites
               PCoA1        PCoA2
VRP_2_1 -0.010418287  0.018869202
VRP_1_3 -0.014215969 -0.012706185
VRP_2_2 -0.007894429  0.039597847
VRP_3_1 -0.006908415 -0.017288518
VRP_3_2 -0.042628112  0.004762452
VRP_1_2 -0.003856702 -0.023998680
VRP_2_3  0.078133558  0.012344215
VRP_3_3 -0.004183521  0.023927699
VRP_1_1  0.011971878 -0.045508032

$centroids
         PCoA1        PCoA2
1 -0.003903216 -0.025013644
2  0.004654079  0.026372346
3 -0.016373164  0.004755486

attr(,"class")
[1] "ordiplot"

[[6]][[2]]
[[6]][[2]]$x
 [1] 0.05946089 0.05248627 0.06793824 0.06535628 0.06661538 0.09864890 0.04643045 0.08063908
 [9] 0.06945883 0.07357559 0.05299429 0.05609351 0.10118141 0.07390286 0.06955294 0.07968234
[17] 0.07220035 0.07874282 0.09956196 0.04938108 0.09413019 0.07123348 0.05844612 0.10263915
[25] 0.06289894 0.07333181 0.06784824 0.12209804 0.06699983 0.09463152 0.09707820 0.07432277
[33] 0.07127660 0.09495626 0.10217575 0.07900144

[[6]][[2]]$y
 [1] 1.452369e-05 1.130464e-06 1.507015e-05 1.515380e-05 1.516122e-05 7.179031e-02
 [7] 5.167531e-07 1.191644e-05 1.565154e-05 9.997450e-06 7.077562e-06 5.647854e-06
[13] 7.179050e-02 1.503238e-05 1.931375e-05 1.600515e-05 1.612818e-05 1.624150e-05
[19] 7.179037e-02 6.427542e-07 1.198406e-05 1.666483e-05 4.634939e-06 7.178089e-02
[25] 1.540911e-05 1.254797e-05 1.264065e-05 7.179748e-02 1.564826e-05 2.359336e-05
[31] 7.178486e-02 1.560133e-05 1.604279e-05 7.179021e-02 7.177840e-02 1.180528e-05

[[6]][[2]]$yf
 [1] 1.452369e-05 1.130464e-06 1.470079e-05 1.470079e-05 1.470079e-05 7.178651e-02
 [7] 5.167531e-07 1.470079e-05 1.470079e-05 1.470079e-05 5.786785e-06 5.786785e-06
[13] 7.178651e-02 1.470079e-05 1.470079e-05 1.470079e-05 1.470079e-05 1.470079e-05
[19] 7.178651e-02 6.427542e-07 1.470079e-05 1.470079e-05 5.786785e-06 7.178651e-02
[25] 1.470079e-05 1.470079e-05 1.470079e-05 7.179748e-02 1.470079e-05 2.359336e-05
[31] 7.178651e-02 1.470079e-05 1.470079e-05 7.178651e-02 7.178651e-02 1.470079e-05


[[6]][[3]]


[[7]]
[[7]][[1]]
$sites
               PCoA1       PCoA2
VRP_1_2  0.025489376 -0.01695810
VRP_1_1 -0.029416857 -0.02347329
VRP_1_3 -0.067611854 -0.01830372
VRP_2_1 -0.007780106 -0.01865890
VRP_2_2  0.044163884 -0.01532530
VRP_2_3  0.035061663 -0.02407526
VRP_3_1  0.059413293  0.04044509
VRP_3_2 -0.049521632  0.04468230
VRP_3_3 -0.009797767  0.03166717

$centroids
         PCoA1       PCoA2
1 -0.027164947 -0.02196136
2  0.026039435 -0.01860575
3 -0.007639575  0.03549524

attr(,"class")
[1] "ordiplot"

[[7]][[2]]
[[7]][[2]]$x
 [1] 0.06589096 0.10429946 0.05421110 0.04161802 0.06753291 0.07491501 0.09923365 0.07649869
 [9] 0.06554872 0.06414838 0.08978431 0.09123432 0.11421035 0.08082159 0.07632782 0.08053750
[17] 0.11937459 0.10512173 0.14165945 0.06706653 0.09009609 0.06548999 0.08301046 0.10237682
[25] 0.08598786 0.06315610 0.07213898 0.06965285 0.11375728 0.08843089 0.07692891 0.12170592
[33] 0.08731839 0.10846902 0.08241560 0.06164845

[[7]][[2]]$y
 [1] 0.06607395 0.11868761 0.03508632 0.04979257 0.05342501 0.09972320 0.12283601 0.08777399
 [9] 0.05950724 0.05618866 0.11547818 0.11141611 0.15868892 0.09398029 0.10049140 0.09463370
[17] 0.16445725 0.16874180 0.19608604 0.06480085 0.10980959 0.07095367 0.08772640 0.10416420
[25] 0.08836906 0.05677084 0.04546062 0.05847038 0.15472595 0.10114573 0.10203778 0.17602239
[33] 0.13413304 0.16670043 0.10175328 0.06577275

[[7]][[2]]$yf
 [1] 0.05981310 0.11868761 0.04243945 0.04243945 0.05981310 0.09516546 0.11414041 0.09516546
 [9] 0.05981310 0.05957742 0.11414041 0.11414041 0.16221428 0.09516546 0.09516546 0.09516546
[17] 0.16445725 0.16221428 0.19608604 0.05981310 0.11414041 0.05981310 0.09516546 0.11414041
[25] 0.09516546 0.05957742 0.05981310 0.05981310 0.16221428 0.11414041 0.09516546 0.17602239
[33] 0.11414041 0.16221428 0.09516546 0.05957742


[[7]][[3]]


[[8]]
[[8]][[1]]
$sites
               PCoA1        PCoA2
VRP_1_1 -0.047020392  0.029430994
VRP_1_2 -0.035494717 -0.005177926
VRP_1_3 -0.038359554  0.003211699
VRP_2_1 -0.004869189 -0.024400240
VRP_2_2 -0.022008899 -0.011857746
VRP_2_3 -0.017321111 -0.005350773
VRP_3_1  0.049753469 -0.006809008
VRP_3_2  0.057954958 -0.021043581
VRP_3_3  0.057365436  0.041996581

$centroids
        PCoA1         PCoA2
1 -0.03969643  0.0073636423
2 -0.01564581 -0.0128541931
3  0.05457603  0.0001890153

attr(,"class")
[1] "ordiplot"

[[8]][[2]]
[[8]][[2]]$x
 [1] 0.07040735 0.07174566 0.08572843 0.07456677 0.07389112 0.11406713 0.12141064 0.11917415
 [9] 0.06146231 0.08145671 0.05425631 0.06591610 0.10233776 0.10419012 0.11415045 0.07625631
[17] 0.05887041 0.06813572 0.10073352 0.11403012 0.11321237 0.05987092 0.05940354 0.08634579
[25] 0.08797748 0.09887814 0.05060967 0.09315227 0.09296135 0.10005260 0.08692778 0.09712586
[33] 0.09761141 0.06080515 0.07559474 0.07829820

[[8]][[2]]$y
 [1] 4.145593e-05 7.040389e-05 1.193093e-04 8.106025e-05 8.269316e-05 7.368306e-02
 [7] 7.369150e-02 7.369674e-02 3.095571e-05 7.988099e-05 4.358615e-05 4.714703e-05
[13] 7.367141e-02 7.367986e-02 7.368514e-02 6.423059e-05 4.017982e-05 4.647528e-05
[19] 7.367735e-02 7.368580e-02 7.369111e-02 3.870566e-05 3.908984e-05 7.362178e-02
[25] 7.363025e-02 7.363558e-02 6.557929e-06 7.363730e-02 7.364575e-02 7.365105e-02
[31] 7.363122e-02 7.363968e-02 7.364498e-02 2.442445e-05 9.073252e-05 6.698293e-05

[[8]][[2]]$yf
 [1] 4.502608e-05 7.040389e-05 1.193093e-04 7.713989e-05 7.713989e-05 7.368628e-02
 [7] 7.369412e-02 7.369412e-02 3.615694e-05 7.988099e-05 3.615694e-05 4.502608e-05
[13] 7.367438e-02 7.367986e-02 7.368628e-02 7.713989e-05 3.615694e-05 4.502608e-05
[19] 7.367438e-02 7.368628e-02 7.368628e-02 3.615694e-05 3.615694e-05 7.362178e-02
[25] 7.363074e-02 7.364066e-02 6.557929e-06 7.364066e-02 7.364066e-02 7.365105e-02
[31] 7.363074e-02 7.364066e-02 7.364066e-02 3.615694e-05 7.713989e-05 7.713989e-05


[[8]][[3]]


[[9]]
[[9]][[1]]
$sites
             PCoA1        PCoA2
VRP_1_3  0.2218044 -0.005636428
VRP_2_1 -0.1277190 -0.167128143
VRP_2_2  0.2650836 -0.008374067
VRP_2_3  0.4096688  0.044302500
VRP_3_1  0.4092775  0.044653939
VRP_1_1 -0.5890577  0.046091100
VRP_1_2 -0.5890577  0.046091100

$centroids
       PCoA1        PCoA2
1 -0.5890577  0.046091100
2  0.2650836 -0.008374074
3  0.4092775  0.044653939

attr(,"class")
[1] "ordiplot"

[[9]][[2]]
[[9]][[2]]$x
 [1] 0.39561404 0.16206897 0.21666667 0.22592593 0.81666667 0.81666667 0.44101633 0.57894737
 [9] 0.57894737 0.50877193 0.50877193 0.20689655 0.20689655 0.86206897 0.86206897 0.08217593
[17] 1.00000000 1.00000000 1.00000000 1.00000000 0.00000000

[[9]][[2]]$y
 [1] 0.777116473 0.074343806 0.667166619 0.707642400 1.600323156 1.592374797 0.792847432
 [8] 0.993447677 1.013069259 0.845786215 0.838813127 0.594957546 0.635635590 1.626693592
[15] 1.618985263 0.041226483 1.802740750 1.797335456 1.815115482 1.809884182 0.009604366

[[9]][[2]]$yf
 [1] 0.777116473 0.074343806 0.667166619 0.707642400 1.600323156 1.592374797 0.792847432
 [8] 0.993447677 1.013069259 0.845786215 0.838813127 0.594957546 0.635635590 1.626693592
[15] 1.618985263 0.041226483 1.802740750 1.797335456 1.815115482 1.809884182 0.009604366


[[9]][[3]]


[[10]]
[[10]][[1]]
$sites
               PCoA1        PCoA2
VRP_2_2  0.003667869  0.011624612
VRP_3_1 -0.008585016 -0.002926648
VRP_3_3 -0.011798764 -0.005512777
VRP_1_1  0.033132381 -0.018166581
VRP_1_2  0.004739255  0.013885028
VRP_1_3 -0.011407492 -0.005143968
VRP_2_1 -0.011138131 -0.005464495
VRP_2_3  0.012923465  0.017121659
VRP_3_2 -0.011533567 -0.005416830

$centroids
          PCoA1         PCoA2
1  0.0047402616 -0.0006787609
2  0.0007645708  0.0068569847
3 -0.0117987452 -0.0055127640

attr(,"class")
[1] "ordiplot"

[[10]][[2]]
[[10]][[2]]$x
 [1] 0.0324616199 0.0326211357 0.0467528872 0.0338651905 0.0327477432 0.0324616199
 [7] 0.0380935505 0.0325450335 0.0152673200 0.0466790462 0.0338651905 0.0189673106
[13] 0.0186073464 0.0380197095 0.0187646009 0.0469124030 0.0338651905 0.0085071263
[19] 0.0056323400 0.0382530663 0.0056323400 0.0471984043 0.0470390105 0.0464597233
[25] 0.0461208522 0.0468363008 0.0338651905 0.0338651905 0.0385390676 0.0338651905
[31] 0.0085071263 0.0383796738 0.0085071263 0.0378003866 0.0003765775 0.0381769641

[[10]][[2]]$y
 [1] 7.550814e-11 6.614260e-11 4.311659e-02 2.465911e-04 6.603371e-11 9.913559e-11
 [7] 1.420358e-03 6.008232e-11 9.604706e-12 4.311659e-02 2.465910e-04 1.313181e-11
[13] 2.367856e-11 1.420358e-03 2.285702e-11 4.311659e-02 2.465910e-04 1.049766e-11
[19] 3.300769e-11 1.420358e-03 1.867982e-11 4.336111e-02 4.311659e-02 4.311659e-02
[25] 4.170208e-02 4.311659e-02 2.465910e-04 2.465910e-04 1.661903e-03 2.465910e-04
[31] 3.516561e-11 1.420358e-03 9.726478e-12 1.420358e-03 4.420091e-11 1.420358e-03

[[10]][[2]]$yf
 [1] 7.338047e-11 7.338047e-11 4.311659e-02 2.465911e-04 7.338047e-11 7.338047e-11
 [7] 1.420358e-03 7.338047e-11 2.205503e-11 4.311659e-02 2.465910e-04 2.205503e-11
[13] 2.205503e-11 1.420358e-03 2.205503e-11 4.311659e-02 2.465910e-04 2.205503e-11
[19] 2.205503e-11 1.420358e-03 2.205503e-11 4.336111e-02 4.311659e-02 4.311659e-02
[25] 4.170208e-02 4.311659e-02 2.465910e-04 2.465910e-04 1.661903e-03 2.465910e-04
[31] 2.205503e-11 1.420358e-03 2.205503e-11 1.420358e-03 2.205503e-11 1.420358e-03


[[10]][[3]]


[[11]]
[[11]][[1]]
$sites
               PCoA1        PCoA2
VRP_1_1 -0.078296780 -0.028806964
VRP_1_2 -0.167802267  0.045825683
VRP_1_3 -0.011252591 -0.007414339
VRP_2_1  0.055271485  0.015156543
VRP_2_2 -0.004217692 -0.027974662
VRP_2_3  0.110587643  0.052597951
VRP_3_1  0.026231806 -0.034657264
VRP_3_2  0.008795153 -0.007345337
VRP_3_3  0.060683244 -0.007381612

$centroids
        PCoA1        PCoA2
1 -0.07867127 -0.008148539
2  0.05512076  0.014506719
3  0.02764335 -0.016480153

attr(,"class")
[1] "ordiplot"

[[11]][[2]]
[[11]][[2]]$x
 [1] 0.14185636 0.11597255 0.15821364 0.11022280 0.21218861 0.14465832 0.13301447 0.16100628
 [9] 0.17653450 0.23526415 0.18605374 0.28176760 0.21271178 0.18993928 0.23967917 0.10331625
[17] 0.06660912 0.14886864 0.08650808 0.08143249 0.11509542 0.10394732 0.09905027 0.09690067
[25] 0.10476192 0.09751349 0.14700768 0.07701766 0.08245111 0.10295656 0.13626823 0.13603139
[33] 0.09903021 0.06766919 0.08751213 0.08073908

[[11]][[2]]$y
 [1] 0.1701724986 0.1208824123 0.2338729522 0.1209455779 0.3300957447 0.1706294193
 [7] 0.1705313760 0.2332303919 0.2711884717 0.3552578530 0.2713047573 0.4697435079
[13] 0.3306241875 0.3306334156 0.3917919783 0.1206405404 0.0001517062 0.2092263075
[19] 0.0625377376 0.0626723921 0.1209466274 0.1206521300 0.1208254490 0.1200861740
[25] 0.1205284534 0.1200039232 0.2091607370 0.0623951050 0.0625294140 0.1208220512
[31] 0.1703381289 0.1706340778 0.1199836013 0.0004428609 0.0626036327 0.0626990573

[[11]][[2]]$yf
 [1] 0.1704190203 0.1209248725 0.2335516721 0.1209248725 0.3303645801 0.1706294193
 [7] 0.1704190203 0.2335516721 0.2711884717 0.3552578530 0.2713047573 0.4697435079
[13] 0.3306241875 0.3303645801 0.3917919783 0.1206937248 0.0001517062 0.2092263075
[19] 0.0626084467 0.0626084467 0.1209248725 0.1206937248 0.1206937248 0.1200245662
[25] 0.1206937248 0.1200245662 0.2091607370 0.0623951050 0.0626084467 0.1206937248
[31] 0.1704190203 0.1704190203 0.1200245662 0.0004428609 0.0626084467 0.0626084467


[[11]][[3]]


[[12]]
[[12]][[1]]
$sites
               PCoA1       PCoA2
VRP_1_1  0.285612011  0.06975416
VRP_2_3 -0.240568520  0.15821396
VRP_3_2 -0.042333316 -0.06888741
VRP_1_2  0.206147707  0.03877824
VRP_1_3  0.019881485 -0.02432232
VRP_2_1  0.009749131 -0.03771493
VRP_2_2  0.083764172 -0.03097856
VRP_3_1 -0.275001651 -0.02511780
VRP_3_3 -0.047251020 -0.07972534

$centroids
         PCoA1       PCoA2
1  0.198679780  0.03683953
2  0.007703531 -0.02387061
3 -0.061074290 -0.07096175

attr(,"class")
[1] "ordiplot"

[[12]][[2]]
[[12]][[2]]$x
 [1] 0.53884609 0.36562165 0.15954177 0.30349773 0.31891641 0.25264980 0.57733887 0.37079417
 [9] 0.30474945 0.47311718 0.33059891 0.33343202 0.38447495 0.21962059 0.31121476 0.29478240
[17] 0.12599723 0.14429100 0.17111566 0.27149518 0.06571064 0.22015673 0.24244383 0.16958518
[25] 0.49227249 0.30966095 0.15033082 0.14983360 0.31815367 0.13291410 0.12404711 0.30710632
[33] 0.15415775 0.37151625 0.18493099 0.27038578

[[12]][[2]]$y
 [1] 0.991854111 0.645912391 0.148576224 0.513163915 0.537916810 0.393605495 1.030278490
 [8] 0.647128790 0.513138030 0.907181053 0.546127015 0.647407253 0.692604501 0.394244339
[15] 0.516052551 0.514094333 0.146438839 0.145236419 0.256180517 0.390921134 0.004070923
[22] 0.392314015 0.396101232 0.257983261 0.903594413 0.514844340 0.144792588 0.148284564
[29] 0.517319407 0.149049761 0.148582720 0.526807345 0.143878783 0.646378927 0.256880205
[36] 0.390664595

[[12]][[2]]$yf
 [1] 0.991854111 0.646659822 0.148576224 0.513465426 0.537916810 0.392975135 1.030278490
 [8] 0.646753858 0.513465426 0.905387733 0.546127015 0.646659822 0.692604501 0.392975135
[15] 0.518755911 0.513465426 0.146609096 0.146609096 0.257014661 0.392975135 0.004070923
[22] 0.392975135 0.392975135 0.257014661 0.905387733 0.518755911 0.146609096 0.146609096
[29] 0.518755911 0.146609096 0.146609096 0.518755911 0.146609096 0.646753858 0.257014661
[36] 0.392975135


[[12]][[3]]


[[13]]
[[13]][[1]]
$sites
                PCoA1        PCoA2
VRP_1_1 -0.0156069532  0.043682824
VRP_1_2 -0.0246628756  0.004058138
VRP_1_3 -0.0271403380  0.003502152
VRP_2_1 -0.0008647333 -0.019163972
VRP_2_2 -0.0142250170 -0.022871057
VRP_2_3 -0.0050351360 -0.021716490
VRP_3_1  0.0307112239  0.012382825
VRP_3_2  0.0311997678  0.007554697
VRP_3_3  0.0256240615 -0.007429117

$centroids
         PCoA1        PCoA2
1 -0.023524336  0.012835024
2 -0.006362871 -0.021143717
3  0.029223573  0.004263319

attr(,"class")
[1] "ordiplot"

[[13]][[2]]
[[13]][[2]]$x
 [1] 0.06205454 0.06395590 0.07041075 0.07311142 0.07472132 0.06908133 0.07137604 0.07988861
 [9] 0.04612878 0.06109659 0.05989634 0.05709941 0.07277572 0.07054681 0.06393194 0.05880214
[17] 0.06434224 0.05752784 0.07376639 0.07297891 0.06770805 0.05025259 0.04892650 0.06367972
[25] 0.06342686 0.05806361 0.05297295 0.06919009 0.07338539 0.07068333 0.06648445 0.06001680
[33] 0.06641512 0.05773842 0.05945587 0.05803279

[[13]][[2]]$y
 [1] 0.033025731 0.032860080 0.052392411 0.059054212 0.045955468 0.045233787 0.052863191
 [8] 0.059349189 0.002708519 0.027425682 0.026898142 0.017142693 0.047765475 0.047407411
[15] 0.045923132 0.029920121 0.028170693 0.019444604 0.050113237 0.050018385 0.048631626
[22] 0.018801299 0.010968763 0.038994244 0.031681149 0.023572293 0.014893445 0.056904911
[29] 0.050431654 0.041938771 0.043344286 0.038675680 0.033096107 0.012310412 0.025070642
[36] 0.013156090

[[13]][[2]]$yf
 [1] 0.032702060 0.035808851 0.049660876 0.051388643 0.051388643 0.046932706 0.050215684
 [8] 0.059349189 0.002708519 0.032702060 0.027296302 0.015958090 0.050215684 0.049660876
[15] 0.035808851 0.027296302 0.035808851 0.015958090 0.051388643 0.050215684 0.046932706
[22] 0.015958090 0.010968763 0.035808851 0.032702060 0.023572293 0.015958090 0.049660876
[29] 0.051388643 0.049660876 0.043344286 0.032702060 0.035808851 0.015958090 0.027296302
[36] 0.015958090


[[13]][[3]]


[[14]]
[[14]][[1]]
$sites
               PCoA1        PCoA2
VRP_3_2  0.008421582 -0.020936817
VRP_3_1  0.036652409  0.014538507
VRP_2_1 -0.002798301 -0.016604044
VRP_2_2 -0.002426286 -0.010846788
VRP_2_3  0.019729565  0.013083993
VRP_3_3  0.021374467  0.019081601
VRP_1_2 -0.008772172 -0.005553182
VRP_1_1 -0.090144852  0.011784855
VRP_1_3  0.017963588 -0.004548125

$centroids
          PCoA1        PCoA2
1 -0.0094166049 -0.004990169
2 -0.0001451989 -0.010408218
3  0.0233550822  0.008994914

attr(,"class")
[1] "ordiplot"

[[14]][[2]]
[[14]][[2]]$x
 [1] 0.05272550 0.02768870 0.02171031 0.04474436 0.04628545 0.04174695 0.10480862 0.03176626
 [9] 0.05338931 0.04894645 0.03531657 0.03592956 0.05425628 0.12793842 0.03821837 0.01652633
[17] 0.04476590 0.05005200 0.02624037 0.09284249 0.03214721 0.04286230 0.04378378 0.03087416
[25] 0.09089354 0.02955082 0.03998968 0.04781716 0.11200956 0.03039168 0.05309800 0.11386331
[33] 0.03725078 0.08717123 0.04030081 0.11047826

[[14]][[2]]$y
 [1] 1.172684e-04 4.545612e-05 3.159810e-05 1.231871e-04 1.222638e-04 9.337321e-05
 [7] 1.369863e-01 6.113762e-05 1.354887e-04 1.265621e-04 7.878096e-05 4.144734e-05
[13] 1.648050e-04 1.371027e-01 6.980314e-05 1.409952e-05 1.123382e-04 1.259018e-04
[19] 4.794394e-05 1.369811e-01 6.636298e-05 1.117257e-04 1.208863e-04 6.182121e-05
[25] 1.369849e-01 5.923787e-05 3.917696e-05 1.178448e-04 1.370920e-01 6.379004e-05
[31] 1.439399e-04 1.371057e-01 6.248008e-05 1.369779e-01 9.648478e-05 1.370433e-01

[[14]][[2]]$yf
 [1] 1.232441e-04 4.670003e-05 3.159810e-05 1.188039e-04 1.200543e-04 9.492900e-05
 [7] 1.369863e-01 6.053337e-05 1.397143e-04 1.232441e-04 6.053337e-05 6.053337e-05
[13] 1.648050e-04 1.371042e-01 6.053337e-05 1.409952e-05 1.188039e-04 1.232441e-04
[19] 4.670003e-05 1.369830e-01 6.053337e-05 1.117257e-04 1.188039e-04 6.053337e-05
[25] 1.369830e-01 5.923787e-05 6.053337e-05 1.200543e-04 1.370920e-01 6.053337e-05
[31] 1.397143e-04 1.371042e-01 6.053337e-05 1.369779e-01 9.492900e-05 1.370433e-01


[[14]][[3]]


[[15]]
[[15]][[1]]
$sites
               PCoA1        PCoA2
VRP_1_2 -0.026841301  0.011363264
VRP_1_3 -0.050267746  0.004659062
VRP_2_1 -0.024898063 -0.041060881
VRP_2_3 -0.017931278 -0.037613303
VRP_3_3  0.076104243  0.020811430
VRP_1_1 -0.102352036  0.045407972
VRP_2_2  0.008860332 -0.036968080
VRP_3_1  0.074477657  0.011570676
VRP_3_2  0.062848193  0.021829861

$centroids
        PCoA1       PCoA2
1 -0.05447831  0.01560738
2 -0.01334609 -0.03829317
3  0.07135836  0.01888926

attr(,"class")
[1] "ordiplot"

[[15]][[2]]
[[15]][[2]]$x
 [1] 0.08473959 0.10010231 0.08706934 0.12596937 0.12342978 0.09751500 0.13199633 0.11997764
 [9] 0.08847274 0.09102040 0.14440484 0.10693615 0.10071408 0.14771231 0.12615928 0.06088207
[17] 0.12880186 0.12694224 0.08287255 0.12946614 0.11821071 0.11726885 0.12482286 0.06226351
[25] 0.11706713 0.11688490 0.18641492 0.10588247 0.07118373 0.05903746 0.14643744 0.18578713
[33] 0.17762483 0.10175621 0.09933862 0.07836007

[[15]][[2]]$y
 [1] 0.002865975 0.120212246 0.119489171 0.124782631 0.124534967 0.120210190 0.126155844
 [8] 0.122997093 0.119805140 0.119113290 0.127064808 0.121846390 0.119880800 0.128421592
[15] 0.125268338 0.001494094 0.124820669 0.124498345 0.003282155 0.124562687 0.123198429
[22] 0.123326622 0.125294220 0.002092996 0.123068967 0.121704336 0.218423008 0.121932121
[29] 0.001812466 0.001955569 0.127360661 0.219055196 0.216474679 0.121651778 0.120324017
[36] 0.003180639

[[15]][[2]]$yf
 [1] 0.003109590 0.120156813 0.119469200 0.124871148 0.124534967 0.120156813 0.126155844
 [8] 0.123174048 0.119469200 0.119469200 0.127064808 0.121827616 0.120156813 0.128421592
[15] 0.124871148 0.001724832 0.124871148 0.124871148 0.003109590 0.124871148 0.123174048
[22] 0.123174048 0.124871148 0.001952731 0.123068967 0.121827616 0.218739102 0.121827616
[29] 0.001952731 0.001724832 0.127360661 0.218739102 0.216474679 0.121651778 0.120156813
[36] 0.003109590


[[15]][[3]]


[[16]]
[[16]][[1]]
$sites
              PCoA1        PCoA2
VRP_1_1 -0.12912773  0.014919557
VRP_1_2 -0.12398326  0.026363299
VRP_3_1 -0.04705503 -0.121009620
VRP_3_3 -0.10883998  0.042921314
VRP_1_3 -0.08709237  0.004051950
VRP_2_1 -0.05144528 -0.025468328
VRP_2_2 -0.08632816 -0.001723691
VRP_3_2 -0.11654287  0.048350178
VRP_2_3  0.75041469  0.011595341

$centroids
        PCoA1       PCoA2
1 -0.11465395  0.01583922
2 -0.03914869 -0.01917113
3 -0.10382557  0.02363153

attr(,"class")
[1] "ordiplot"

[[16]][[2]]
[[16]][[2]]$x
 [1] 0.10805227 0.18410319 0.13900472 0.11935255 0.14265616 0.12809462 0.12587721 0.88313342
 [9] 0.19118181 0.13742821 0.11491675 0.15512800 0.12601363 0.14085309 0.87864655 0.18594097
[17] 0.14603310 0.12800543 0.15016857 0.19136278 0.80890973 0.10300059 0.12389418 0.11514055
[25] 0.08396771 0.86287654 0.10380084 0.08219937 0.10011870 0.83934294 0.10410117 0.13267105
[33] 0.80562158 0.11248810 0.83957518 0.87025116

[[16]][[2]]$y
 [1]   0.12445152   0.15773938   0.05687559   0.09021877   0.08331357   0.09884692
 [7]   0.06533217 361.46198517   0.24863556   0.06760507   0.08605588   0.15116373
[13]   0.09294472   0.06024447 361.42010756   0.19562993   0.16664327   0.09757719
[19]   0.16402046   0.20623136 361.36661211   0.06426585   0.10291695   0.07488416
[25]   0.01060460 361.44411066   0.07005978   0.01062040   0.07076438 361.38130382
[31]   0.06925300   0.11324580 361.38412162   0.08128672 361.37087866 361.44806846

[[16]][[2]]$yf
 [1]   0.08638663   0.15989171   0.08638663   0.08638663   0.08638663   0.08638663
 [7]   0.08638663 361.46198517   0.22743346   0.08638663   0.08638663   0.15989171
[13]   0.08638663   0.08638663 361.43742889   0.19562993   0.15989171   0.08638663
[19]   0.15989171   0.22743346 361.37536687   0.06751512   0.08638663   0.08638663
[25]   0.01061250 361.43742889   0.06965639   0.01061250   0.06751512 361.37609124
[31]   0.06965639   0.08638663 361.37536687   0.08638663 361.37609124 361.43742889


[[16]][[3]]


[[17]]
[[17]][[1]]
$sites
               PCoA1        PCoA2
VRP_1_1  0.062107545 -0.037740411
VRP_1_2 -0.030214045 -0.029643538
VRP_1_3  0.086600042  0.007985490
VRP_2_1  0.004405502 -0.013286614
VRP_2_2 -0.072467053 -0.005408393
VRP_2_3 -0.047223862 -0.015288095
VRP_3_1 -0.075638046  0.037051825
VRP_3_2  0.069218605  0.035193772
VRP_3_3  0.003211311  0.021135965

$centroids
        PCoA1       PCoA2
1  0.05646762 -0.02889193
2 -0.03755355 -0.01199711
3  0.00316067  0.02179559

attr(,"class")
[1] "ordiplot"

[[17]][[2]]
[[17]][[2]]$x
 [1] 0.10162273 0.06591117 0.08198579 0.15089154 0.12650980 0.15726581 0.08923962 0.09646000
 [9] 0.13255407 0.05650580 0.06870077 0.06765814 0.09440398 0.12207841 0.06961997 0.10034433
[17] 0.16533422 0.14665758 0.16966472 0.06267847 0.10175429 0.09618121 0.07806267 0.10842552
[25] 0.08804399 0.06176993 0.08667708 0.07764806 0.15421615 0.10740195 0.08475413 0.13932022
[33] 0.08187881 0.15570791 0.09741892 0.08432889

[[17]][[2]]$y
 [1] 0.13775726 0.07310506 0.09550029 0.22878515 0.18595251 0.26668594 0.11517051 0.13899792
 [9] 0.18623190 0.04959500 0.09219700 0.06492794 0.13845501 0.16893661 0.09491767 0.13700546
[17] 0.27784644 0.21705465 0.29512753 0.07264569 0.14639486 0.14084901 0.09065825 0.17128881
[25] 0.12235496 0.06935458 0.08452368 0.09322455 0.25256932 0.16298009 0.08075612 0.17769063
[33] 0.08279556 0.24807885 0.15244757 0.09612966

[[17]][[2]]$yf
 [1] 0.14240343 0.07022623 0.09007809 0.22878515 0.18329168 0.26668594 0.11876273 0.13992346
 [9] 0.18329168 0.04959500 0.09007809 0.07022623 0.13845501 0.17011271 0.09007809 0.14240343
[17] 0.27784644 0.21705465 0.29512753 0.07022623 0.14639486 0.13992346 0.09007809 0.17011271
[25] 0.11876273 0.06935458 0.09007809 0.09007809 0.25032409 0.16298009 0.09007809 0.18329168
[33] 0.09007809 0.25032409 0.14240343 0.09007809


[[17]][[3]]


[[18]]
[[18]][[1]]
$sites
              PCoA1        PCoA2
VRP_3_3  0.06782801 -0.035330182
VRP_1_1 -0.06694854  0.061075726
VRP_1_2 -0.27099063 -0.023001237
VRP_1_3  0.03036859  0.011924289
VRP_2_1  0.05853868  0.040030489
VRP_2_2  0.02000853  0.030530311
VRP_2_3  0.08795823 -0.006333070
VRP_3_1  0.04167647 -0.001687456
VRP_3_2  0.03156066 -0.077208870

$centroids
        PCoA1       PCoA2
1 -0.06803463  0.05416469
2  0.05647768  0.02881967
3  0.05339190 -0.03757433

attr(,"class")
[1] "ordiplot"

[[18]][[2]]
[[18]][[2]]$x
 [1] 0.16867758 0.34231712 0.08175996 0.10328657 0.09825592 0.07098349 0.06099132 0.05891458
 [9] 0.23163666 0.12998747 0.15847241 0.12368672 0.18318577 0.13921078 0.17583737 0.30822067
[17] 0.33681366 0.29896449 0.36128886 0.31519346 0.30869892 0.08469924 0.06261895 0.10047301
[25] 0.05348674 0.09869034 0.07269115 0.07451242 0.07266831 0.13228544 0.10561606 0.06351432
[33] 0.11658405 0.07221525 0.10359702 0.08203917

[[18]][[2]]$y
 [1] 3.538298e-04 4.703164e-01 1.018733e-04 1.329529e-04 1.426967e-04 4.635069e-05
 [7] 5.222287e-05 6.511205e-05 4.703218e-01 2.560678e-04 2.545198e-04 2.113881e-04
[13] 3.606985e-04 3.016353e-04 4.091406e-04 4.703422e-01 4.702439e-01 4.703120e-01
[19] 4.702702e-01 4.703156e-01 4.703525e-01 9.916011e-05 5.347813e-05 1.246869e-04
[25] 5.343880e-05 1.530809e-04 7.484154e-05 1.176250e-04 9.299083e-05 1.980623e-04
[31] 1.517025e-04 9.048402e-05 2.009512e-04 7.166414e-05 9.684349e-05 1.126251e-04

[[18]][[2]]$yf
 [1] 3.538298e-04 4.703093e-01 1.078209e-04 1.300522e-04 1.300522e-04 6.841736e-05
 [7] 5.693768e-05 5.693768e-05 4.703093e-01 2.270651e-04 2.780776e-04 2.113881e-04
[13] 3.849195e-04 2.780776e-04 3.849195e-04 4.703093e-01 4.703093e-01 4.703093e-01
[19] 4.703093e-01 4.703093e-01 4.703093e-01 1.078209e-04 5.693768e-05 1.300522e-04
[25] 5.343880e-05 1.300522e-04 8.391619e-05 1.078209e-04 8.391619e-05 2.270651e-04
[31] 1.517025e-04 6.841736e-05 2.009512e-04 7.166414e-05 1.300522e-04 1.078209e-04


[[18]][[3]]


[[19]]
[[19]][[1]]
$sites
                PCoA1        PCoA2
VRP_2_2 -0.0266066570 -0.001924197
VRP_1_3 -0.0749825196  0.020006172
VRP_3_2  0.0569976754 -0.001395119
VRP_3_3 -0.0110483540 -0.063660496
VRP_1_2 -0.0496615022 -0.006473644
VRP_2_1  0.0110712512 -0.028139431
VRP_2_3  0.0007964805  0.027013331
VRP_3_1  0.0864768332  0.005205835
VRP_1_1  0.0069567926  0.049367548

$centroids
         PCoA1        PCoA2
1 -0.047994013  0.014936042
2 -0.008175006  0.002042303
3  0.054854314 -0.007580292

attr(,"class")
[1] "ordiplot"

[[19]][[2]]
[[19]][[2]]$x
 [1] 0.06631031 0.09417298 0.06999634 0.04539349 0.06281311 0.04943648 0.11823346 0.06468467
 [9] 0.13784673 0.10595172 0.05677512 0.10423959 0.08714526 0.16533447 0.08314118 0.09540643
[17] 0.11538898 0.06834988 0.07555813 0.06105225 0.06915638 0.07585823 0.06423947 0.09748769
[25] 0.12168792 0.11471033 0.08035455 0.06546200 0.13994604 0.08423123 0.06700693 0.09464130
[33] 0.08574203 0.09525646 0.03660271 0.09281513

[[19]][[2]]$y
 [1] 0.09175780 0.14068969 0.11679918 0.04817891 0.07961175 0.05406343 0.18689146 0.07840507
 [9] 0.22666197 0.18691435 0.06468234 0.17065956 0.11447452 0.26296831 0.12428062 0.16532663
[17] 0.18748799 0.09036588 0.11695703 0.06263536 0.12249024 0.12223201 0.07934168 0.15859967
[25] 0.22766688 0.18366512 0.11540909 0.09679543 0.23506534 0.11776883 0.09641360 0.15102668
[33] 0.11831314 0.14849529 0.02551281 0.14303752

[[19]][[2]]$yf
 [1] 0.09383318 0.14186361 0.11874718 0.04817891 0.07911950 0.05406343 0.18718972 0.07911950
 [9] 0.22716443 0.18528973 0.06365885 0.17065956 0.11874718 0.26296831 0.11874718 0.16196315
[17] 0.18718972 0.09383318 0.11874718 0.06365885 0.11874718 0.11874718 0.07911950 0.16196315
[25] 0.22716443 0.18528973 0.11874718 0.09383318 0.23506534 0.11874718 0.09383318 0.14976098
[33] 0.11874718 0.14976098 0.02551281 0.14186361


[[19]][[3]]

Remove dissimilar replicates

Based on the output from 04-filter-ASV-by-SODM.Rmd, I now want to filter the dataset to remove replicates for loci that have high dissimilarity values, listed here: /data/reference_pool_dissimilarity_samples_to_remove.csv.

# bind together the vouchered and full reference SODM dataframes
reference_df_sodm_filtered <- vrp_sodm_filtered_df %>% bind_rows(frp_sodm_filtered_df)

A clean, non-redundant version of the reference sample dataframe

ref_sodm_filtered_unique <- reference_df_sodm_filtered %>% 
  select(locus, seq, sample, count) %>%
  unique() %>% # if there are multiple entries with different counts, we want to collapse those reads
  group_by(locus, seq, sample) %>%
  mutate(total_reads = sum(count)) %>%
  select(-count) %>%
  rename(count = total_reads)

So that is the dataframe from which we want to remove this particular list of locus-samples

# read in the list of samples to remove
tossers <- read_csv("../data/reference_pool_dissimilarity_samples_to_remove.csv")
Parsed with column specification:
cols(
  locus = col_character(),
  sample = col_character()
)

It turns out that an anti-join is all I need for this filtering step.

ref_sodm_bray_filtered_unique <- ref_sodm_filtered_unique %>%
  anti_join(., tossers, by = c("locus", "sample")) 

Okay, so that is the dataset that I can work through the assessment analyses with, beginning with summary statistics, then adding in the taxonomy and assessing true/false positives in the vouchered samples and breadth of taxonomic coverage in the full reference pool.

Save filtered dataframe

Save the filtered feature table output from occupancy modeling and dissimilarity

# save this version of the feature table to combine with taxonomy for locus-integrated taxonomy
ref_sodm_bray_filtered_unique %>%
  saveRDS("../data/feature_table_sodm_bray_filtered.rds", compress = "xz")
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